changing docs to say digest

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: tximeta
-Version: 1.21.3
+Version: 1.21.4
 Title: Transcript Quantification Import with Automatic Metadata
 Description: Transcript quantification import from Salmon and
     other quantifiers with automatic attachment of transcript ranges

NEWS.md

@@ -1,3 +1,7 @@
+# tximeta 1.21.4
+
+* Changing language in docs to "digest" instead of "checksum".
+
 # tximeta 1.21.3
 
 * GENCODE 44 (H.s.), M34 (M.m), and Ensembl 111

R/linkedTxome.R

@@ -1,6 +1,6 @@
 #' Make and load linked transcriptomes ("linkedTxome")
 #'
-#' \code{makeLinkedTxome} reads the checksum associated with a Salmon
+#' \code{makeLinkedTxome} reads the digest associated with a Salmon
 #' index at \code{indexDir}, and links it to key information
 #' about the transcriptome, including the \code{source}, \code{organism},
 #' \code{release}, and \code{genome} (these are custom character strings),
@@ -58,7 +58,7 @@
 #' on Zenodo. This enables consistent annotation and downstream annotation
 #' tasks, such as by \code{summarizeToGene}.
 #' @param write logical, should a JSON file be written out
-#' which documents the transcriptome checksum and metadata? (default is TRUE)
+#' which documents the transcriptome digest and metadata? (default is TRUE)
 #' @param jsonFile the path to the json file for the linkedTxome
 #'
 #' @return nothing, the function is run for its side effects

R/tximeta.R

@@ -55,7 +55,7 @@ NULL
 
 #' Import transcript quantification with metadata
 #' 
-#' \code{tximeta} leverages the hashed checksum of the Salmon or piscem index,
+#' \code{tximeta} leverages the hashed digest of the Salmon or piscem index,
 #' in addition to a number of core Bioconductor packages (GenomicFeatures,
 #' ensembldb, AnnotationHub, GenomeInfoDb, BiocFileCache) to automatically
 #' populate metadata for the user, without additional effort from the user.
@@ -66,11 +66,11 @@ NULL
 #' \code{tximeta} can be used with any quantification \code{type} that is supported
 #' by \code{\link{tximport}}, where it will return an non-ranged SummarizedExperiment.
 #' 
-#' \code{tximeta} performs a lookup of the hashed checksum of the index
+#' \code{tximeta} performs a lookup of the hashed digest of the index
 #' (stored in an auxilary information directory of the Salmon output)
 #' against a database of known transcriptomes, which lives within the tximeta
 #' package and is continually updated on Bioconductor's release schedule.
-#' In addition, \code{tximeta} performs a lookup of the checksum against a
+#' In addition, \code{tximeta} performs a lookup of the digest against a
 #' locally stored table of \code{linkedTxome}'s (see \code{link{makeLinkedTxome}}).
 #' If \code{tximeta} detects a match, it will automatically populate,
 #' e.g. the transcript locations, the transcriptome release,
@@ -142,7 +142,7 @@ NULL
 #' @param ... arguments passed to \code{tximport}
 #' 
 #' @return a SummarizedExperiment with metadata on the \code{rowRanges}.
-#' (if the hashed checksum in the Salmon or Sailfish index does not match
+#' (if the hashed digest in the Salmon or Sailfish index does not match
 #' any known transcriptomes, or any locally saved \code{linkedTxome},
 #' \code{tximeta} will just return a non-ranged SummarizedExperiment)
 #'
@@ -486,7 +486,7 @@ may lead to errors in object construction, unless 'dropInfReps=TRUE'")
 missingMetadata <- function(se, summarize=FALSE) {
   msg <- "use of this function requires transcriptome metadata which is missing.
   either: (1) the object was not produced by tximeta, or
-  (2) tximeta could not recognize the checksum of the transcriptome.
+  (2) tximeta could not recognize the digest of the transcriptome.
   If (2), use a linkedTxome to provide the missing metadata and rerun tximeta"
   if (summarize) {
     msg <- paste0(msg, "

README.md

@@ -26,8 +26,9 @@ This metadata is attached to the *SummarizedExperiment* in the
 `metadata()` and `rowRanges()` slots.
 
 For a list of the reference transcriptomes supported by `tximeta()`,
-see the "Pre-computed checksums" section of the vignette in the 
-`Get started` tab.
+see the "Pre-computed digests" section of the vignette in the 
+`Get started` tab. We call the computed identifier for the reference
+transcriptome a "digest" or sometimes a "checksum".
 
 Further steps are also facilitated, e.g. `summarizeToGene()`, `addIds()`,
 or even `retrieveCDNA()` (the transcripts used for quantification) or

vignettes/tximeta.Rmd

@@ -125,10 +125,16 @@ se <- tximeta(coldata)
 
 # What happened? 
 
-`tximeta` recognized the hashed checksum of the transcriptome that the files
-were quantified against, it accessed the GTF file of the transcriptome
-source, found and attached the transcript ranges, and added the
-appropriate transcriptome and genome metadata.  A remote GTF is only
+`tximeta` recognized the computed *digest* of the transcriptome that
+the files were quantified against, it accessed the GTF file of the
+transcriptome source, found and attached the transcript ranges, and
+added the appropriate transcriptome and genome metadata.
+A *digest* is a small string of alphanumeric characters that uniquely
+identifies the collection of sequences that were used for
+quantification (it is the application of a hash function). We
+sometimes also call this value a "checksum" (in the tximeta paper).
+
+A remote GTF is only
 downloaded once, and a local or remote GTF is only parsed to build a
 *TxDb* or *EnsDb* once: if `tximeta` recognizes that it has seen this *Salmon*
 index before, it will use a cached version of the metadata and
@@ -158,13 +164,13 @@ downloading the GTF file. Again, the download/construction of a
 transcript database occurs only once, and upon subsequent usage of
 *tximeta* functions, the cached version will be used.
 
-# Pre-computed checksums
+# Pre-computed digests
 
 We plan to support a wide variety of sources and organisms for
-transcriptomes with pre-computed checksums, though for now the
+transcriptomes with pre-computed digests, though for now the
 software focuses on predominantly human and mouse transcriptomes 
 
-The following checksums are supported in this version of `tximeta`:
+The following digests are supported in this version of `tximeta`:
 
 ```{r echo=FALSE}
 dir2 <- system.file("extdata", package="tximeta")
@@ -492,11 +498,11 @@ e.g. if R gave an error when trying to connect to the TxDb associated
 with GENCODE v99 human transcripts, you should look for the `rid` of
 the entry associated with the human v99 GTF from GENCODE.
 
-# What if checksum isn't known?
+# What if digest isn't known?
 
 `tximeta` automatically imports relevant metadata when the
 transcriptome matches a known source -- *known* in the sense that it
-is in the set of pre-computed hashed checksums in `tximeta` (GENCODE,
+is in the set of pre-computed hashed digests in `tximeta` (GENCODE,
 Ensembl, and RefSeq for human and mouse). `tximeta` also facilitates the
 linking of transcriptomes used in building the *Salmon* index with
 relevant public sources, in the case that these are not part of this
@@ -511,7 +517,7 @@ automatically recognized by `tximeta` and does not require making a
 out support for all common transcriptomes, from all sources.
 
 **Note:** if you are using Salmon in alignment mode, then there is no
-Salmon index, and without the Salmon index, there is no checksum. We
+Salmon index, and without the Salmon index, there is no digest. We
 don't have a perfect solution for this yet, but you can still
 summarize transcript counts to gene with a `tx2gene` table that you
 construct manually (see `tximport` vignette for example code). 
@@ -562,7 +568,7 @@ of these cases.
 To make this quantification reproducible, we make a `linkedTxome`
 which records key information about the sources of the transcript
 FASTA files, and the location of the relevant GTF file. It also
-records the checksum of the transcriptome that was computed by
+records the digest of the transcriptome that was computed by
 *Salmon* during the `index` step.
 
 **Source:** when creating the `linkedTxome` one must specify the 
@@ -595,7 +601,7 @@ the gene identifier to an underscore. See
 
 
 By default, `linkedTxome` will write out a JSON file which can be
-shared with others, linking the checksum of the index with the other
+shared with others, linking the digest of the index with the other
 metadata, including FASTA and GTF sources. By default, it will write
 out to a file with the same name as the `indexDir`, but with a `.json`
 extension added. This can be prevented with `write=FALSE`, and the
@@ -669,7 +675,7 @@ makeLinkedTxome(indexDir=indexDir,
 ```
 
 After running `makeLinkedTxome`, the connection between this *Salmon*
-index (and its checksum) with the sources is saved for persistent
+index (and its digest) with the sources is saved for persistent
 usage. Note that because we added a single transcript of 960bp to the
 FASTA file used for quantification, `tximeta` could tell that this was
 not quantified against release 98 of the Ensembl transcripts for