drseqCount: Construct DrSeq Data

In fchen365/surf: Statistical Utility for RBP (RNA binding protein) Functions

Description

This function creates the drseqData slot needed by DrSeq analysis, which is a DEXSeq::DEXSeqDataSet. This function requires two DrSeq annotation files created by prepDrseqAnno. Two files have the same prefix (anno.prefix), the same suffix (anno.format), and only differ by "exon/event". If annotation files are missing, this function can create them freshly, which might take some time. This function counts the RNA-seq reads on ATR events and genes using featureCounts.

Usage

drseqCount(
  event,
  sampleData,
  design = ~sample + exon + condition:exon,
  remove.overlap.exon = FALSE,
  anno.prefix = "drseq.annotation",
  anno.format = "gff2",
  minMQS = 10,
  isPairedEnd = TRUE,
  cores = max(1, detectCores() - 2),
  verbose = FALSE,
  ...
)

Arguments

event	a surf object from parseEvent.
sampleData	data.frame, describes the RNA-seq samples and contains at least two columns – bam and condition, whose row.names represent sample names.
design	A formula which specifies the design of the experiment. It must specify an interaction term between a variable from the sampleData columns with the 'exon' variable. By default, the design will be '~ sample + exon + condition:exon'. This formula indicates the contrast between 'condition' and exon', i.e. differences in exon usage due to changes in the 'condition' variable. See the vignette for more examples of other designs.
remove.overlap.exon	logical, remove overlapping exons across genes (default to FALSE).
anno.prefix	character, file names for outputting annotation files. If prefix is absent, hidden file will be output to the current working directory.
anno.format	character, e.g. "gtf", as accepted by rtracklayer::export.
minMQS, isPairedEnd	as defined in Rsubread::featureCounts. Note that the default is customized for SURF (see details for more information).
cores	integer, number of available workers, sent to nthreads of featureCounts.
verbose	logical, whether (TRUE) to echo progress.
...	additional parameters for Rsubread::featureCounts.

Details

If you used Illumina HiSeq 2000, set strandSpecific = 2 (reversed strand).

Value

a surf object, with drseqData slot updated.

fchen365/surf documentation built on June 18, 2021, 12:02 p.m.