From 3ce2bb735473970c651e0cc4b70b193a7e8966c1 Mon Sep 17 00:00:00 2001 From: Mike Love Date: Mon, 26 Aug 2024 09:25:29 -0400 Subject: [PATCH] add index --- index.html | 751 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 751 insertions(+) create mode 100644 index.html diff --git a/index.html b/index.html new file mode 100644 index 0000000..d0f3b14 --- /dev/null +++ b/index.html @@ -0,0 +1,751 @@ + + + + + + + + + + +Bioconductor cheat sheet + + + + + + + + + + + + + + + + + + + +
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Bioconductor cheat sheet

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Author
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Michael Love

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Install

+

For details go to http://bioconductor.org/install/

+
if (!requireNamespace("BiocManager"))
+    install.packages("BiocManager")
+BiocManager::install()
+BiocManager::install(c("package1","package2")
+BiocManager::valid() # are packages up to date?
+
+# what Bioc version is release right now?
+http://bioconductor.org/bioc-version
+# what Bioc versions are release/devel?
+http://bioconductor.org/js/versions.js
+
+
+

help within R

+

Simple help:

+
?functionName
+?"eSet-class" # classes need the '-class' on the end
+help(package="foo",help_type="html") # launch web browser help
+vignette("topic")
+browseVignettes(package="package") # show vignettes for the package
+

Help for advanced users:

+
functionName # prints source code
+getMethod(method,"class")  # prints source code for method
+selectMethod(method, "class") # will climb the inheritance to find method
+showMethods(classes="class") # show all methods for class
+methods(class="GRanges") # this will work in R >= 3.2
+?"functionName,class-method" # method help for S4 objects, e.g.:
+?"plotMA,data.frame-method" # from library(geneplotter)
+?"method.class" # method help for S3 objects e.g.:
+?"plot.lm"
+sessionInfo() # necessary info for getting help
+packageVersion("foo") # what version of package
+

Bioconductor support website: https://support.bioconductor.org

+

If you use RStudio, then you already get nicely rendered documentation using ? or help. If you are a command line person, then you can use this alias to pop up a help page in your web browser with rhelp functionName packageName.

+
alias rhelp="Rscript -e 'args <- commandArgs(TRUE); help(args[2], package=args[3], help_type=\"html\"); Sys.sleep(5)' --args"
+
+
+

debugging R

+
traceback() # what steps lead to an error
+# debug a function
+debug(myFunction) # step line-by-line through the code in a function
+undebug(myFunction) # stop debugging
+debugonce(myFunction) # same as above, but doesn't need undebug()
+# also useful if you are writing code is to put
+# the function browser() inside a function at a critical point
+# this plus devtools::load_all() can be useful for programming
+# to jump in function on error:
+options(error=recover)
+# turn that behavior off:
+options(error=NULL)
+# debug, e.g. estimateSizeFactors from DESeq2...
+# debugging an S4 method is more difficult; this gives you a peek inside:
+trace(estimateSizeFactors, browser, exit=browser, signature="DESeqDataSet")
+
+
+

Show package-specific methods for a class

+

These two long strings of R code do approximately the same thing: obtain the methods that operate on an object of a given class, which are defined in a specific package.

+
intersect(sapply(strsplit(as.character(methods(class="DESeqDataSet")), ","), `[`, 1), ls("package:DESeq2"))
+sub("Function: (.*) \\(package .*\\)","\\1",grep("Function",showMethods(classes="DESeqDataSet", where=getNamespace("DESeq2"), printTo=FALSE), value=TRUE))
+
+
+

Annotations

+

For AnnotationHub examples, see:

+

https://www.bioconductor.org/help/workflows/annotation/Annotation_Resources

+

The following is how to work with the organism database packages, and biomart.

+

AnnotationDbi

+
# using one of the annotation packges
+library(AnnotationDbi)
+library(org.Hs.eg.db) # or, e.g. Homo.sapiens
+columns(org.Hs.eg.db)
+keytypes(org.Hs.eg.db)
+head(keys(org.Hs.eg.db, keytype="ENTREZID"))
+# returns a named character vector, see ?mapIds for multiVals options
+res <- mapIds(org.Hs.eg.db, keys=k, column="ENSEMBL", keytype="ENTREZID")
+
+# generates warning for 1:many mappings
+res <- select(org.Hs.eg.db, keys=k,
+  columns=c("ENTREZID","ENSEMBL","SYMBOL"),
+  keytype="ENTREZID")
+

biomaRt

+
# map from one annotation to another using biomart
+library(biomaRt)
+m <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
+map <- getBM(mart = m,
+  attributes = c("ensembl_gene_id", "entrezgene"),
+  filters = "ensembl_gene_id", 
+  values = some.ensembl.genes)
+
+
+

Genomic ranges

+

GenomicRanges

+
library(GenomicRanges)
+z <- GRanges("chr1",IRanges(1000001,1001000),strand="+")
+start(z)
+end(z)
+width(z)
+strand(z)
+mcols(z) # the 'metadata columns', any information stored alongside each range
+ranges(z) # gives the IRanges
+seqnames(z) # the chromosomes for each ranges
+seqlevels(z) # the possible chromosomes
+seqlengths(z) # the lengths for each chromosome
+
+

Intra-range methods

+

Affects ranges independently

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functiondescription
shiftmoves left/right
narrownarrows by relative position within range
resizeresizes to width, fixing start for +, end for -
flankreturns flanking ranges to the left +, or right -
promoterssimilar to flank
restrictrestricts ranges to a start and end position
trimtrims out of bound ranges
+/-expands/contracts by adding/subtracting fixed amount
*zooms in (positive) or out (negative) by multiples
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+

Inter-range methods

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Affects ranges as a group

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functiondescription
rangeone range, leftmost start to rightmost end
reducecover all positions with only one range
gapsuncovered positions within range
disjoinbreaks into discrete ranges based on original starts/ends
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+
+

Nearest methods

+

Given two sets of ranges, x and subject, for each range in x, returns…

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functiondescription
nearestindex of the nearest neighbor range in subject
precedeindex of the range in subject that is directly preceded by the range in x
followindex of the range in subject that is directly followed by the range in x
distanceToNearestdistances to its nearest neighbor in subject (Hits object)
distancedistances to nearest neighbor (integer vector)
+

A Hits object can be accessed with queryHits, subjectHits and mcols if a distance is associated.

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+
+

set methods

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If y is a GRangesList, then use punion, etc. All functions have default ignore.strand=FALSE, so are strand specific.

+
union(x,y) 
+intersect(x,y)
+setdiff(x,y)
+
+
+

Overlaps

+
x %over% y  # logical vector of which x overlaps any in y
+fo <- findOverlaps(x,y) # returns a Hits object
+queryHits(fo)   # which in x
+subjectHits(fo) # which in y
+
+
+

Seqnames and seqlevels

+

GenomicRanges and GenomeInfoDb

+
gr.sub <- gr[seqlevels(gr) == "chr1"]
+seqlevelsStyle(x) <- "UCSC" # convert to 'chr1' style from "NCBI" style '1'
+
+
+
+

Sequences

+

Biostrings

+

see the Biostrings Quick Overview PDF

+

For naming, see cheat sheet for annotation

+
library(BSgenome.Hsapiens.UCSC.hg19)
+dnastringset <- getSeq(Hsapiens, granges) # returns a DNAStringSet
+# also Views() for Bioconductor >= 3.1
+
library(Biostrings)
+dnastringset <- readDNAStringSet("transcripts.fa")
+
substr(dnastringset, 1, 10) # to character string
+subseq(dnastringset, 1, 10) # returns DNAStringSet
+Views(dnastringset, 1, 10) # lightweight views into object
+complement(dnastringset)
+reverseComplement(dnastringset)
+matchPattern("ACGTT", dnastring) # also countPattern, also works on Hsapiens/genome
+vmatchPattern("ACGTT", dnastringset) # also vcountPattern
+letterFrequecy(dnastringset, "CG") # how many C's or G's
+# also letterFrequencyInSlidingView
+alphabetFrequency(dnastringset, as.prob=TRUE)
+# also oligonucleotideFrequency, dinucleotideFrequency, trinucleotideFrequency
+# transcribe/translate for imitating biological processes
+
+
+

Sequencing data

+

Rsamtools scanBam returns lists of raw values from BAM files

+
library(Rsamtools)
+which <- GRanges("chr1",IRanges(1000001,1001000))
+what <- c("rname","strand","pos","qwidth","seq")
+param <- ScanBamParam(which=which, what=what)
+# for more BamFile functions/details see ?BamFile
+# yieldSize for chunk-wise access
+bamfile <- BamFile("/path/to/file.bam")
+reads <- scanBam(bamfile, param=param)
+res <- countBam(bamfile, param=param) 
+# for more sophisticated counting modes
+# see summarizeOverlaps() below
+
+# quickly check chromosome names
+seqinfo(BamFile("/path/to/file.bam"))
+
+# DNAStringSet is defined in the Biostrings package
+# see the Biostrings Quick Overview PDF
+dnastringset <- scanFa(fastaFile, param=granges)
+

GenomicAlignments returns Bioconductor objects (GRanges-based)

+
library(GenomicAlignments)
+ga <- readGAlignments(bamfile) # single-end
+ga <- readGAlignmentPairs(bamfile) # paired-end
+
+
+

Transcript databases

+

GenomicFeatures

+
# get a transcript database, which stores exon, trancript, and gene information
+library(GenomicFeatures)
+library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
+
+# or build a txdb from GTF file (e.g. downloadable from Ensembl FTP site)
+txdb <- makeTranscriptDbFromGFF("file.GTF", format="gtf")
+
+# or build a txdb from Biomart (however, not as easy to reproduce later)
+txdb <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
+
+# in Bioconductor >= 3.1, also makeTxDbFromGRanges
+
+# saving and loading
+saveDb(txdb, file="txdb.sqlite")
+loadDb("txdb.sqlite")
+
+# extracting information from txdb
+g <- genes(txdb) # GRanges, just start to end, no exon/intron information
+tx <- transcripts(txdb) # GRanges, similar to genes()
+e <- exons(txdb) # GRanges for each exon
+ebg <- exonsBy(txdb, by="gene") # exons grouped in a GRangesList by gene
+ebt <- exonsBy(txdb, by="tx") # similar but by transcript
+
+# then get the transcript sequence
+txSeq <- extractTranscriptSeqs(Hsapiens, ebt)
+
+
+

Summarizing information across ranges and experiments

+

The SummarizedExperiment is a storage class for high-dimensional information tied to the same GRanges or GRangesList across experiments (e.g., read counts in exons for each gene).

+
library(GenomicAlignments)
+fls <- list.files(pattern="*.bam$")
+library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
+ebg <- exonsBy(txdb, by="gene")
+# see yieldSize argument for restricting memory
+bf <- BamFileList(fls)
+library(BiocParallel)
+register(MulticoreParam(4))
+# lots of options in the man page
+# singleEnd, ignore.strand, inter.features, fragments, etc.
+se <- summarizeOverlaps(ebg, bf)
+
+# operations on SummarizedExperiment
+assay(se) # the counts from summarizeOverlaps
+colData(se)
+rowRanges(se)
+

My preferred quantification method is Salmon, with --gcBias option enabled unless you know there is no GC dependence in the data, followed by tximport. Here is an example of usage:

+
coldata <- read.table("samples.txt")
+rownames(coldata) <- coldata$id
+files <- coldata$files; names(files) <- coldata$id
+txi <- tximport(files, type="salmon", tx2gene=tx2gene)
+dds <- DESeqDataSetFromTximport(txi, coldata, ~condition)
+

Another fast Bioconductor read counting method is featureCounts in Rsubread.

+
library(Rsubread)
+res <- featureCounts(files, annot.ext="annotation.gtf",
+  isGTFAnnotationFile=TRUE,
+  GTF.featureType="exon",
+  GTF.attrType="gene_id")
+res$counts
+
+
+

RNA-seq gene-wise analysis

+

DESeq2

+

My preferred pipeline for DESeq2 users is to start with a lightweight transcript abundance quantifier such as Salmon and to use tximport, followed by DESeqDataSetFromTximport.

+

Here, coldata is a data.frame with group as a column.

+
library(DESeq2)
+# from tximport
+dds <- DESeqDataSetFromTximport(txi, coldata, ~ group)
+# from SummarizedExperiment
+dds <- DESeqDataSet(se, ~ group)
+# from count matrix
+dds <- DESeqDataSetFromMatrix(counts, coldata, ~ group)
+# minimal filtering helps keep things fast 
+# one can set 'n' to e.g. min(5, smallest group sample size)
+keep <- rowSums(counts(dds) >= 10) >= n 
+dds <- dds[keep,]
+dds <- DESeq(dds)
+res <- results(dds) # no shrinkage of LFC, or:
+res <- lfcShrink(dds, coef = 2, type="apeglm") # shrink LFCs
+

edgeR

+
# this chunk from the Quick start in the edgeR User Guide
+library(edgeR) 
+y <- DGEList(counts=counts,group=group)
+keep <- filterByExpr(y)
+y <- y[keep,]
+y <- calcNormFactors(y)
+design <- model.matrix(~group)
+y <- estimateDisp(y,design)
+fit <- glmFit(y,design)
+lrt <- glmLRT(fit)
+topTags(lrt)
+# or use the QL methods:
+qlfit <- glmQLFit(y,design)
+qlft <- glmQLFTest(qlfit)
+topTags(qlft)
+

limma-voom

+
library(limma)
+design <- model.matrix(~ group)
+y <- DGEList(counts)
+keep <- filterByExpr(y)
+y <- y[keep,]
+y <- calcNormFactors(y)
+v <- voom(y,design)
+fit <- lmFit(v,design)
+fit <- eBayes(fit)
+topTable(fit)
+

Many more RNA-seq packages

+
+
+

Expression set

+
library(Biobase)
+data(sample.ExpressionSet)
+e <- sample.ExpressionSet
+exprs(e)
+pData(e)
+fData(e)
+
+
+

Get GEO dataset

+
library(GEOquery)
+e <- getGEO("GSE9514")
+
+
+

Microarray analysis

+
library(affy)
+library(limma)
+phenoData <- read.AnnotatedDataFrame("sample-description.csv")
+eset <- justRMA("/celfile-directory", phenoData=phenoData)
+design <- model.matrix(~ Disease, pData(eset))
+fit <- lmFit(eset, design)
+efit <- eBayes(fit)
+topTable(efit, coef=2)
+
+
+

iCOBRA performance metrics

+
library(iCOBRA)
+cd <- COBRAData(pval=pval.df, padj=padj.df, score=score.df, truth=truth.df)
+cp <- calculate_performance(cd, binary_truth = "status", cont_truth = "logFC")
+cobraplot <- prepare_data_for_plot(cp)
+plot_fdrtprcurve(cobraplot)
+# interactive shiny app:
+COBRAapp(cd)
+
+ +
+ + +
+ + + + \ No newline at end of file