diff --git a/404.html b/404.html index f5750e7..bde3db3 100644 --- a/404.html +++ b/404.html @@ -18,7 +18,7 @@ - +
@@ -52,7 +52,7 @@
  • - +
    • @@ -63,7 +63,7 @@
    - +
    @@ -91,16 +91,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 7f758d4..5fc45dd 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -3,7 +3,7 @@ - +
    @@ -34,14 +34,14 @@
    - +
    @@ -106,15 +106,15 @@

    Attribution -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/index.html b/articles/index.html index bdb5f38..5118d76 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,7 +3,7 @@ - +
    @@ -34,14 +34,14 @@
    - +
    @@ -65,15 +65,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/tximeta.html b/articles/tximeta.html index 820a086..001d02a 100644 --- a/articles/tximeta.html +++ b/articles/tximeta.html @@ -12,14 +12,13 @@ - - +
    @@ -53,7 +52,7 @@
  • - +
    • @@ -64,7 +63,7 @@
    - +
    @@ -74,9 +73,9 @@

    Tximeta: transcript quantification import with

    Michael I. Love, Charlotte Soneson, Peter F. Hickey, Rob Patro

    -

    06/08/2024

    +

    09/27/2024

    - Source: vignettes/tximeta.Rmd + Source: vignettes/tximeta.Rmd
    @@ -120,7 +119,7 @@

    Introductionother quantifiers section below.

    -

    +

    Tximeta import starts with sample table @@ -408,7 +407,7 @@

    Retrieve the transcript database -
    ## loading existing TxDb created: 2024-06-08 13:09:13
    +
    ## loading existing TxDb created: 2024-09-27 15:45:37
    ## Loading required package: GenomicFeatures
    ## Loading required package: AnnotationDbi
    @@ -443,7 +442,7 @@ 
    Add exons per transcript
 
-
    ## loading existing TxDb created: 2024-06-08 13:09:13
    
+
    ## loading existing TxDb created: 2024-09-27 15:45:37
    
 
    ## generating exon ranges
    
 
     rowRanges(se.exons)[[1]]
    
@@ -482,7 +481,7 @@ 
    Easy summarization to gene-leveltx_ids.
    
 
     gse <- summarizeToGene(se)
    
-
    ## loading existing TxDb created: 2024-06-08 13:09:13
    
+
    ## loading existing TxDb created: 2024-09-27 15:45:37
    
 
    ## obtaining transcript-to-gene mapping from database
    
 
    ## generating gene ranges
    
 
    ## assignRanges='range': gene ranges assigned by total range of isoforms
@@ -541,7 +540,7 @@ 
    Assign ranges by abundance
-
    
+

    @@ -640,9 +639,9 @@

    Differential expression analysis 
     gse <- summarizeToGene(se, countsFromAbundance="lengthScaledTPM")
    -
    ## loading existing TxDb created: 2024-06-08 13:09:13
    +
    ## loading existing TxDb created: 2024-09-27 15:45:37
    ## obtaining transcript-to-gene mapping from database
    -
    ## loading existing gene ranges created: 2024-06-08 13:09:17
    +
    ## loading existing gene ranges created: 2024-09-27 15:45:41
    ## assignRanges='range': gene ranges assigned by total range of isoforms
 ##   see details at: ?summarizeToGene,SummarizedExperiment-method
    ## summarizing abundance
    @@ -720,9 +719,9 @@

    Additional metadatastr(metadata(se)[["tximetaInfo"]])

    ## List of 3
 ##  $ version   :Classes 'package_version', 'numeric_version'  hidden list of 1
-##   ..$ : int [1:3] 1 23 2
+##   ..$ : int [1:3] 1 23 4
 ##  $ type      : chr "salmon"
-##  $ importTime: POSIXct[1:1], format: "2024-06-08 13:09:05"
    +## $ importTime: POSIXct[1:1], format: "2024-09-27 15:45:28" 
     str(metadata(se)[["txdbInfo"]])
    ##  Named chr [1:13] "TxDb" "GenomicFeatures" ...
@@ -920,7 +919,7 @@ 
    Linked transcriptomes                release="98", genome="BDGP6.22",
                 fasta=fastaFTP, gtf=gtfPath,
                 jsonFile=jsonFile)
    -
    ## writing linkedTxome to /tmp/RtmpLZTW6v/Dm.BDGP6.22.98.plus_salmon-0.14.1.json
    +
    ## writing linkedTxome to /tmp/RtmpfTcwNs/Dm.BDGP6.22.98.plus_salmon-0.14.1.json
    ## saving linkedTxome in bfc

    After running makeLinkedTxome, the connection between this Salmon index (and its digest) with the sources is saved @@ -1029,13 +1028,13 @@

    Clear linkedTxomes## # A tibble: 7 × 10 ## rid rname create_time access_time rpath rtype fpath last_modified_time etag ## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> -## 1 BFC1 link… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA -## 2 BFC2 Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA -## 3 BFC3 txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA -## 4 BFC4 exon… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA -## 5 BFC5 gene… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA -## 6 BFC6 Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA -## 7 BFC7 txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d… NA NA +## 1 BFC1 link… 2024-09-27… 2024-09-27… /tmp… rela… 1576… NA NA +## 2 BFC2 Dros… 2024-09-27… 2024-09-27… /tmp… rela… 1576… NA NA +## 3 BFC3 txpR… 2024-09-27… 2024-09-27… /tmp… rela… 1576… NA NA +## 4 BFC4 exon… 2024-09-27… 2024-09-27… /tmp… rela… 1576… NA NA +## 5 BFC5 gene… 2024-09-27… 2024-09-27… /tmp… rela… 1576… NA NA +## 6 BFC6 Dros… 2024-09-27… 2024-09-27… /tmp… rela… 1576… NA NA +## 7 BFC7 txpR… 2024-09-27… 2024-09-27… /tmp… rela… 1576… NA NA ## # ℹ 1 more variable: expires <dbl> 
     bfcremove(bfc, bfcquery(bfc, "linkedTxomeTbl")$rid)
@@ -1043,12 +1042,12 @@ 
    Clear linkedTxomes## # A tibble: 6 × 10
 ##   rid   rname create_time access_time rpath rtype fpath last_modified_time etag 
 ##   <chr> <chr> <chr>       <chr>       <chr> <chr> <chr>              <dbl> <chr>
-## 1 BFC2  Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 2 BFC3  txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 3 BFC4  exon… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 4 BFC5  gene… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 5 BFC6  Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 6 BFC7  txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 1 BFC2  Dros… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 2 BFC3  txpR… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 3 BFC4  exon… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 4 BFC5  gene… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 5 BFC6  Dros… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 6 BFC7  txpR… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
 ## # ℹ 1 more variable: expires <dbl>
    @@ -1078,8 +1077,8 @@

    Loading linkedTxome JSON files< 
    ## 1 
 ## found matching linked transcriptome:
 ## [ LocalEnsembl - Drosophila melanogaster - release 98 ]
-## loading existing TxDb created: 2024-06-08 13:09:29
-## loading existing transcript ranges created: 2024-06-08 13:09:29
    +## loading existing TxDb created: 2024-09-27 15:45:54 +## loading existing transcript ranges created: 2024-09-27 15:45:54     
    ## Warning in checkAssays2Txps(assays, txps): 
 ## 
 ## Warning: the annotation is missing some transcripts that were quantified.
@@ -1110,13 +1109,13 @@ 
    Clear linkedTxomes again## # A tibble: 7 × 10
 ##   rid   rname create_time access_time rpath rtype fpath last_modified_time etag 
 ##   <chr> <chr> <chr>       <chr>       <chr> <chr> <chr>              <dbl> <chr>
-## 1 BFC2  Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 2 BFC3  txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 3 BFC4  exon… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 4 BFC5  gene… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 5 BFC6  Dros… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 6 BFC7  txpR… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
-## 7 BFC8  link… 2024-06-08… 2024-06-08… /tmp… rela… 125d…                 NA NA   
+## 1 BFC2  Dros… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 2 BFC3  txpR… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 3 BFC4  exon… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 4 BFC5  gene… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 5 BFC6  Dros… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 6 BFC7  txpR… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
+## 7 BFC8  link… 2024-09-27… 2024-09-27… /tmp… rela… 1576…                 NA NA   
 ## # ℹ 1 more variable: expires <dbl>
    @@ -1209,7 +1208,7 @@

    Session infosession_info()

    ## ─ Session info ───────────────────────────────────────────────────────────────
 ##  setting  value
-##  version  R version 4.4.0 (2024-04-24)
+##  version  R version 4.4.1 (2024-06-14)
 ##  os       Ubuntu 22.04.4 LTS
 ##  system   x86_64, linux-gnu
 ##  ui       X11
@@ -1217,147 +1216,147 @@ 
    Session info##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       UTC
-##  date     2024-06-08
-##  pandoc   3.1.13 @ /usr/bin/ (via rmarkdown)
+##  date     2024-09-27
+##  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
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 ## 
 ##  [1] /__w/_temp/Library
 ##  [2] /usr/local/lib/R/site-library
@@ -1417,9 +1416,7 @@ 
    References
 
-        
-

    + @@ -1432,16 +1429,16 @@

    References

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/authors.html b/authors.html index dd8460e..e22f96b 100644 --- a/authors.html +++ b/authors.html @@ -3,7 +3,7 @@ - +
    @@ -34,14 +34,14 @@
    - +
    @@ -50,36 +50,36 @@

    Authors and Citation

    - +

    Citation

    - Source: inst/CITATION + Source: inst/CITATION
    @@ -107,15 +107,15 @@

    Citation

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/index.html b/index.html index fb93856..907f9e5 100644 --- a/index.html +++ b/index.html @@ -19,7 +19,7 @@ - +
    @@ -53,7 +53,7 @@
  • - +
    • @@ -64,7 +64,7 @@
    - +
    @@ -171,16 +171,16 @@

    Developers

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/news/index.html b/news/index.html index b7e4cb4..0642135 100644 --- a/news/index.html +++ b/news/index.html @@ -3,7 +3,7 @@ - +
    @@ -34,20 +34,20 @@
    - +

    Changelog

    - Source: NEWS.md + Source: NEWS.md
    @@ -141,15 +141,15 @@

    tximeta 1.2.0
    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/pkgdown.yml b/pkgdown.yml index 9224807..2652135 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,10 +1,9 @@ -pandoc: 3.1.13 -pkgdown: 2.0.9 +pandoc: '3.2' +pkgdown: 2.1.1 pkgdown_sha: ~ articles: tximeta: tximeta.html -last_built: 2024-06-08T13:08Z +last_built: 2024-09-27T15:44Z urls: reference: https://thelovelab.github.io/tximeta/reference article: https://thelovelab.github.io/tximeta/articles - diff --git a/reference/Rplot001.png b/reference/Rplot001.png deleted file mode 100644 index 17a3580..0000000 Binary files a/reference/Rplot001.png and /dev/null differ diff --git a/reference/addCDS.html b/reference/addCDS.html index f0de416..ff88897 100644 --- a/reference/addCDS.html +++ b/reference/addCDS.html @@ -16,7 +16,7 @@ - +
    @@ -47,20 +47,20 @@
    - +

    Add CDS to rowRanges of a transcript-level SummarizedExperiment

    - Source: R/addRanges.R + Source: R/addRanges.R
    @@ -87,15 +87,15 @@

    Add CDS to rowRanges of a transcript-level SummarizedExperiment

    Arguments

    -
    se
    + + +
    se

    the SummarizedExperiment

    Value

    - - -

    a SummarizedExperiment

    +

    a SummarizedExperiment

    @@ -110,15 +110,15 @@

    Value

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/addExons.html b/reference/addExons.html index 5f29a6c..012ce9c 100644 --- a/reference/addExons.html +++ b/reference/addExons.html @@ -11,7 +11,7 @@ - +
    @@ -42,20 +42,20 @@
    - +

    Add exons to rowRanges of a transcript-level SummarizedExperiment

    - Source: R/addRanges.R + Source: R/addRanges.R
    @@ -77,15 +77,15 @@

    Add exons to rowRanges of a transcript-level SummarizedExperiment

    Arguments

    -
    se
    + + +
    se

    the SummarizedExperiment

    Value

    - - -

    a SummarizedExperiment

    +

    a SummarizedExperiment

    Details

    @@ -113,15 +113,15 @@

    Details

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/addIds.html b/reference/addIds.html index 252b710..15342d7 100644 --- a/reference/addIds.html +++ b/reference/addIds.html @@ -8,7 +8,7 @@ - +
    @@ -39,20 +39,20 @@
    - +

    Add IDs to rowRanges of a SummarizedExperiment

    - Source: R/addIds.R + Source: R/addIds.R
    @@ -71,38 +71,38 @@

    Add IDs to rowRanges of a SummarizedExperiment

    Arguments

    -
    se
    + + +
    se

    the SummarizedExperiment

    -
    column
    +
    column

    the name of the new ID to add (a column of the org package database or of the TxDb/EnsDb is fromDb=TRUE)

    -
    fromDb
    +
    fromDb

    logical, whether to use the TxDb/EnsDb that is associated with se. Default is FALSE, and an org package is used. Currently only implemented for transcript level (gene=FALSE). Column names can be viewed with columns(retrieveDb(se))

    -
    gene
    +
    gene

    logical, whether to map by genes or transcripts (default is FALSE). if rows are genes, and easily detected as such (ENSG or ENSMUSG), it will automatically switch to TRUE. if rows are transcripts and gene=TRUE, then it will try to use a gene_id column to map IDs to column

    -
    ...
    +
    ...

    arguments passed to mapIds

    Value

    - - -

    a SummarizedExperiment

    +

    a SummarizedExperiment

    @@ -221,15 +221,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/getTximetaBFC.html b/reference/getTximetaBFC.html index 63be27d..e7629b3 100644 --- a/reference/getTximetaBFC.html +++ b/reference/getTximetaBFC.html @@ -8,7 +8,7 @@ - +
    @@ -39,20 +39,20 @@
    - +

    Get or set the directory of the BiocFileCache used by tximeta

    - Source: R/bfcLocation.R + Source: R/bfcLocation.R
    @@ -73,21 +73,21 @@

    Get or set the directory of the BiocFileCache used by tximeta

    Arguments

    -
    dir
    + + +
    dir

    the location for tximeta's BiocFileCache. can be missing in which case the function will call file.choose for choosing location interactively

    -
    quiet
    +
    quiet

    whether to suppress feedback message

    Value

    - - -

    the directory of the BiocFileCache used by tximeta +

    the directory of the BiocFileCache used by tximeta (or nothing, in the case of setTximetaBFC)

    @@ -117,15 +117,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/index.html b/reference/index.html index 50af4e0..38f3436 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,9 +1,9 @@ -Function reference • tximetaPackage index • tximeta - +
    @@ -34,14 +34,14 @@
    - +
    @@ -134,15 +134,15 @@

    Other helpers
    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/linkedTxome.html b/reference/linkedTxome.html index b9182bc..a41e194 100644 --- a/reference/linkedTxome.html +++ b/reference/linkedTxome.html @@ -9,7 +9,7 @@ - +
    @@ -40,20 +40,20 @@
    - +

    Make and load linked transcriptomes ("linkedTxome")

    - Source: R/linkedTxome.R + Source: R/linkedTxome.R
    @@ -85,11 +85,13 @@

    Make and load linked transcriptomes ("linkedTxome")

    Arguments

    -
    indexDir
    + + +
    indexDir

    the local path to the Salmon index

    -
    source
    +
    source

    the source of transcriptome (e.g. "de-novo"). Note: if you specify "GENCODE" or "Ensembl", this will trigger behavior by tximeta that may not be desired: e.g. attempts to @@ -103,25 +105,25 @@

    Arguments

    with the Ensembl GTF.

    -
    organism
    +
    organism

    organism (e.g. "Homo sapiens")

    -
    release
    +
    release

    release number (e.g. "27")

    -
    genome
    +
    genome

    genome (e.g. "GRCh38", or "none")

    -
    fasta
    +
    fasta

    location(s) for the FASTA transcript sequences (of which the transcripts used to build the index is equal or a subset). This can be a local path, or an HTTP or FTP URL

    -
    gtf
    +
    gtf

    location for the GTF/GFF file (of which the transcripts used to build the index is equal or a subset). This can be a local path, or an HTTP or FTP URL @@ -137,20 +139,18 @@

    Arguments

    tasks, such as by summarizeToGene.

    -
    write
    +
    write

    logical, should a JSON file be written out which documents the transcriptome digest and metadata? (default is TRUE)

    -
    jsonFile
    +
    jsonFile

    the path to the json file for the linkedTxome

    Value

    - - -

    nothing, the function is run for its side effects

    +

    nothing, the function is run for its side effects

    Details

    @@ -220,15 +220,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/loadLinkedTxome.html b/reference/loadLinkedTxome.html new file mode 100644 index 0000000..62b7e57 --- /dev/null +++ b/reference/loadLinkedTxome.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/makeDGEList.html b/reference/makeDGEList.html index e6880fb..52da082 100644 --- a/reference/makeDGEList.html +++ b/reference/makeDGEList.html @@ -5,7 +5,7 @@ - +
    @@ -36,20 +36,20 @@
    - +

    Make a DGEList from tximeta output

    - Source: R/dgelist.R + Source: R/dgelist.R
    @@ -65,15 +65,15 @@

    Make a DGEList from tximeta output

    Arguments

    -
    se
    + + +
    se

    a SummarizedExperiment produced by tximeta

    Value

    - - -

    a DGEList

    +

    a DGEList

    @@ -88,15 +88,15 @@

    Value

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/makeLinkedTxome.html b/reference/makeLinkedTxome.html new file mode 100644 index 0000000..62b7e57 --- /dev/null +++ b/reference/makeLinkedTxome.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/retrieveCDNA.html b/reference/retrieveCDNA.html index 1707046..7622f2b 100644 --- a/reference/retrieveCDNA.html +++ b/reference/retrieveCDNA.html @@ -8,7 +8,7 @@ - +
    @@ -39,20 +39,20 @@
    - +

    Retrieve the cDNA transcript sequence for a SummarizedExperiment

    - Source: R/retrievers.R + Source: R/retrievers.R
    @@ -71,29 +71,29 @@

    Retrieve the cDNA transcript sequence for a SummarizedExperiment

    Arguments

    -
    se
    + + +
    se

    the SummarizedExperiment

    -
    quiet
    +
    quiet

    logical, suppress messages

    Value

    - - -

    a DNAStringSet object

    +

    a DNAStringSet object

    Examples

    
-if (FALSE) {
+if (FALSE) { # \dontrun{
 # this example is not run because it requires access to Ensembl ftp
 example(tximeta)
 cdna <- retrieveCDNA(se)
-}
+} # }
    @@ -109,15 +109,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/retrieveDb.html b/reference/retrieveDb.html index c2f3775..b8bc1ed 100644 --- a/reference/retrieveDb.html +++ b/reference/retrieveDb.html @@ -7,7 +7,7 @@ - +
    @@ -38,20 +38,20 @@
    - +

    Retrieve the TxDb or EnsDb associated with a SummarizedExperiment

    - Source: R/retrievers.R + Source: R/retrievers.R
    @@ -69,15 +69,15 @@

    Retrieve the TxDb or EnsDb associated with a SummarizedExperiment

    Arguments

    -
    se
    + + +
    se

    the SummarizedExperiment

    Value

    - - -

    a database object

    +

    a database object

    @@ -115,11 +115,11 @@

    Examples

    #> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-06-08 13:08:47 +#> loading existing TxDb created: 2024-09-27 15:45:09 #> Loading required package: GenomicFeatures #> Loading required package: GenomeInfoDb #> Loading required package: GenomicRanges -#> loading existing transcript ranges created: 2024-06-08 13:08:48 +#> loading existing transcript ranges created: 2024-09-27 15:45:09 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified. @@ -140,7 +140,7 @@

    Examples

    #> tximet> #> tximet> edb <- retrieveDb(se) -#> loading existing TxDb created: 2024-06-08 13:08:47 +#> loading existing TxDb created: 2024-09-27 15:45:09
    @@ -156,15 +156,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/setTximetaBFC.html b/reference/setTximetaBFC.html new file mode 100644 index 0000000..37d0a77 --- /dev/null +++ b/reference/setTximetaBFC.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/reference/splitSE.html b/reference/splitSE.html index 7e280b0..21a2d49 100644 --- a/reference/splitSE.html +++ b/reference/splitSE.html @@ -1,15 +1,15 @@ -Split SummarizedExperiment by gene categories — splitSE • tximetaSplit SummarizedExperiment by gene categories — splitSE • tximeta - +
    @@ -40,28 +40,28 @@
    - +

    Split SummarizedExperiment by gene categories

    - Source: R/splitSE.R + Source: R/splitSE.R
    -

    Construct a new SummarizedExperiment by splitting one of the assays -into a list of assays, each of which contains features of a given -'type'. It is assumed that there is a one-to-one correspondence -between feature sets of different types; for example, these can be +

    Construct a new SummarizedExperiment by splitting one of the assays +into a list of assays, each of which contains features of a given +'type'. It is assumed that there is a one-to-one correspondence +between feature sets of different types; for example, these can be spliced and unspliced variants of the same transcripts. The type of each feature in the original SummarizedExperiment, and the correspondence between the features of different types, are given in a data.frame.

    @@ -73,34 +73,32 @@

    Split SummarizedExperiment by gene categories

    Arguments

    -
    se
    + + +
    se

    A SummarizedExperiment object.

    -
    splitDf
    -

    A data.frame with feature IDs. Each column -represents a separate feature type, and the features in a given -row are considered representatives of the same feature (and will +

    splitDf
    +

    A data.frame with feature IDs. Each column +represents a separate feature type, and the features in a given +row are considered representatives of the same feature (and will be represented as one feature in the output object).

    -
    assayName
    +
    assayName

    A character scalar, indicating the assay of se that will be split. Must be one of assayNames(se).

    Value

    - - -

    A SummarizedExperiment object with the same columns - as the input object, and the same number of assays as the number - of columns in splitDf. The assays will be named by the - column names of splitDf. The colData and metadata

    - - -

    of the input SummarizedExperiment object are copied to the - output object. The row names are set to the feature IDs in the +

    A SummarizedExperiment object with the same columns + as the input object, and the same number of assays as the number + of columns in splitDf. The assays will be named by the + column names of splitDf. The colData and metadata + of the input SummarizedExperiment object are copied to the + output object. The row names are set to the feature IDs in the first column of splitDf.

    @@ -137,15 +135,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/summarizeToGene.html b/reference/summarizeToGene.html index 30ac272..5cd8f75 100644 --- a/reference/summarizeToGene.html +++ b/reference/summarizeToGene.html @@ -11,7 +11,7 @@ - +
    @@ -42,20 +42,20 @@
    - +

    Summarize estimated quantitites to gene-level

    - Source: R/summarizeToGene.R + Source: R/summarizeToGene.R
    @@ -72,7 +72,7 @@

    Summarize estimated quantitites to gene-level

    - 
    # S4 method for SummarizedExperiment
+    
    # S4 method for class 'SummarizedExperiment'
 summarizeToGene(
   object,
   assignRanges = c("range", "abundant"),
@@ -83,11 +83,13 @@ 
    Summarize estimated quantitites to gene-level
    
 
     
    
     
    Arguments
    
-    
    object
    
+
+
+
    object
    
 
    a SummarizedExperiment produced by tximeta
    
 
 
-
    assignRanges
    
+
    assignRanges
    
 
    "range" or "abundant", this argument
 controls the way that the rowRanges of the output object are assigned
 (note that this argument does not affect data aggregation at all).
@@ -102,23 +104,19 @@ 
    Arguments
    
 isoform proportions) are also returned in mcols
    
 
 
-
    varReduce
    
+
    varReduce
    
 
    whether to reduce per-sample inferential replicates
 information into a matrix of sample variances variance (default FALSE)
    
 
 
-
    ...
    
+
    ...
    
 
    arguments passed to tximport
    
 
 
    
     
    
     
    Value
    
-    
-
-
    a SummarizedExperiment with summarized quantifications
+    
    a SummarizedExperiment with summarized quantifications
 and transcript IDs as a CharacterList in the mcols
    
-
-
     
    
 
     
    
@@ -156,8 +154,8 @@ 
    Examples
    
 #> 
 #> found matching linked transcriptome:
 #> [ LocalEnsembl - Drosophila melanogaster - release 98 ]
-#> loading existing TxDb created: 2024-06-08 13:08:47
-#> loading existing transcript ranges created: 2024-06-08 13:08:48
+#> loading existing TxDb created: 2024-09-27 15:45:09
+#> loading existing transcript ranges created: 2024-09-27 15:45:09
 #> Warning: 
 #> 
 #> Warning: the annotation is missing some transcripts that were quantified.
@@ -178,7 +176,7 @@ 
    Examples
    
 #> tximet> 
 #> tximet> 
 gse <- summarizeToGene(se)
-#> loading existing TxDb created: 2024-06-08 13:08:47
+#> loading existing TxDb created: 2024-09-27 15:45:09
 #> obtaining transcript-to-gene mapping from database
 #> generating gene ranges
 #> assignRanges='range': gene ranges assigned by total range of isoforms
@@ -201,15 +199,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/reference/tximeta-package.html b/reference/tximeta-package.html
index e69c648..87c8bd2 100644
--- a/reference/tximeta-package.html
+++ b/reference/tximeta-package.html
@@ -12,7 +12,7 @@
 
 
 
-    
+
 
     
    
       
    
 
@@ -43,20 +43,20 @@
    - +

    Import transcript quantification with metadata

    - Source: R/tximeta.R + Source: R/tximeta.R
    @@ -122,15 +122,15 @@

    Author

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/tximeta.html b/reference/tximeta.html index 5a35257..2d73071 100644 --- a/reference/tximeta.html +++ b/reference/tximeta.html @@ -7,7 +7,7 @@ - +
    @@ -38,20 +38,20 @@
    - +

    Import transcript quantification with metadata

    - Source: R/tximeta.R + Source: R/tximeta.R
    @@ -74,24 +74,27 @@

    Import transcript quantification with metadata

    markDuplicateTxps = FALSE, cleanDuplicateTxps = FALSE, customMetaInfo = NULL, + skipFtp = FALSE, ... )

    Arguments

    -
    coldata
    + + +
    coldata

    a data.frame with at least two columns (others will propogate to object):

    • files - character, paths of quantification files

    • names - character, sample names

    if coldata is a vector, it is assumed to be the paths of quantification files and unique sample names are created

    -
    type
    +
    type

    what quantifier was used (see tximport)

    -
    txOut
    +
    txOut

    whether to output transcript-level data. tximeta is designed to have transcript-level output with Salmon, so default is TRUE, @@ -102,27 +105,27 @@

    Arguments

    produces only gene-level quantification).

    -
    skipMeta
    +
    skipMeta

    whether to skip metadata generation (e.g. to avoid errors if not connected to internet). This calls tximport directly and so either txOut=TRUE or tx2gene should be specified.

    -
    skipSeqinfo
    +
    skipSeqinfo

    whether to skip the addition of Seqinfo, which requires an internet connection to download the relevant chromosome information table from UCSC

    -
    useHub
    +
    useHub

    whether to first attempt to download a TxDb/EnsDb object from AnnotationHub, rather than creating from a GTF file from FTP (default is TRUE). If FALSE, it will force tximeta to download and parse the GTF

    -
    markDuplicateTxps
    +
    markDuplicateTxps

    whether to mark the status (hasDuplicate) and names of duplicate transcripts (duplicates) in the rowData of the SummarizedExperiment output. @@ -130,14 +133,14 @@

    Arguments

    of the number of transcripts sets per gene (numDupSets)

    -
    cleanDuplicateTxps
    +
    cleanDuplicateTxps

    whether to try to clean duplicate transcripts (exact sequence duplicates) by replacing the transcript names that do not appear in the GTF with those that do appear in the GTF

    -
    customMetaInfo
    +
    customMetaInfo

    the relative path to a custom metadata information JSON file, relative to the paths in files of coldata. For example, customMetaInfo="meta_info.json" @@ -148,15 +151,18 @@

    Arguments

    (see details in vignette).

    -
    ...
    +
    skipFtp
    +

    whether to avoid ftp:// in case of +firewall, default is FALSE

    + + +
    ...

    arguments passed to tximport

    Value

    - - -

    a SummarizedExperiment with metadata on the rowRanges. +

    a SummarizedExperiment with metadata on the rowRanges. (if the hashed digest in the Salmon or Sailfish index does not match any known transcriptomes, or any locally saved linkedTxome, tximeta will just return a non-ranged SummarizedExperiment)

    @@ -222,8 +228,8 @@

    Examples

    #> #> found matching linked transcriptome: #> [ LocalEnsembl - Drosophila melanogaster - release 98 ] -#> loading existing TxDb created: 2024-06-08 13:08:47 -#> loading existing transcript ranges created: 2024-06-08 13:08:48 +#> loading existing TxDb created: 2024-09-27 15:45:09 +#> loading existing transcript ranges created: 2024-09-27 15:45:09 #> Warning: #> #> Warning: the annotation is missing some transcripts that were quantified. @@ -254,15 +260,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/sitemap.xml b/sitemap.xml index 7ae1057..0aeacaa 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,63 +1,23 @@ - - - - https://thelovelab.github.io/tximeta/404.html - - - https://thelovelab.github.io/tximeta/CODE_OF_CONDUCT.html - - - https://thelovelab.github.io/tximeta/articles/index.html - - - https://thelovelab.github.io/tximeta/articles/tximeta.html - - - https://thelovelab.github.io/tximeta/authors.html - - - https://thelovelab.github.io/tximeta/index.html - - - https://thelovelab.github.io/tximeta/news/index.html - - - https://thelovelab.github.io/tximeta/reference/addCDS.html - - - https://thelovelab.github.io/tximeta/reference/addExons.html - - - https://thelovelab.github.io/tximeta/reference/addIds.html - - - https://thelovelab.github.io/tximeta/reference/getTximetaBFC.html - - - https://thelovelab.github.io/tximeta/reference/index.html - - - https://thelovelab.github.io/tximeta/reference/linkedTxome.html - - - https://thelovelab.github.io/tximeta/reference/makeDGEList.html - - - https://thelovelab.github.io/tximeta/reference/retrieveCDNA.html - - - https://thelovelab.github.io/tximeta/reference/retrieveDb.html - - - https://thelovelab.github.io/tximeta/reference/splitSE.html - - - https://thelovelab.github.io/tximeta/reference/summarizeToGene.html - - - https://thelovelab.github.io/tximeta/reference/tximeta-package.html - - - https://thelovelab.github.io/tximeta/reference/tximeta.html - + +https://thelovelab.github.io/tximeta/404.html +https://thelovelab.github.io/tximeta/CODE_OF_CONDUCT.html +https://thelovelab.github.io/tximeta/articles/index.html +https://thelovelab.github.io/tximeta/articles/tximeta.html +https://thelovelab.github.io/tximeta/authors.html +https://thelovelab.github.io/tximeta/index.html +https://thelovelab.github.io/tximeta/news/index.html +https://thelovelab.github.io/tximeta/reference/addCDS.html +https://thelovelab.github.io/tximeta/reference/addExons.html +https://thelovelab.github.io/tximeta/reference/addIds.html +https://thelovelab.github.io/tximeta/reference/getTximetaBFC.html +https://thelovelab.github.io/tximeta/reference/index.html +https://thelovelab.github.io/tximeta/reference/linkedTxome.html +https://thelovelab.github.io/tximeta/reference/makeDGEList.html +https://thelovelab.github.io/tximeta/reference/retrieveCDNA.html +https://thelovelab.github.io/tximeta/reference/retrieveDb.html +https://thelovelab.github.io/tximeta/reference/splitSE.html +https://thelovelab.github.io/tximeta/reference/summarizeToGene.html +https://thelovelab.github.io/tximeta/reference/tximeta-package.html +https://thelovelab.github.io/tximeta/reference/tximeta.html +