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

Description Usage Arguments Value References

Perform the differential REU (DrSeq) test in a single command. This function is a wrapper that calls the necessary functions in order for DrSeq.

drseq(
  event,
  sampleData,
  design = ~sample + exon + condition:exon,
  remove.overlap.exon = FALSE,
  anno.prefix = "drseq.annotation",
  anno.format = "gff2",
  minMQS = 10,
  isPairedEnd = TRUE,
  ...,
  fullModel = design,
  reducedModel = ~sample + exon,
  fitExpToVar = "condition",
  drseq.fdr = 0.05,
  read.length = 100,
  min.adjMean = 0.05,
  filter.overlap.event = TRUE,
  cores = max(1, detectCores() - 2),
  verbose = FALSE
)

`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`	as defined in Rsubread::featureCounts. Note that the default is customized for SURF (see details for more information).
`isPairedEnd`	as defined in Rsubread::featureCounts. Note that the default is customized for SURF (see details for more information).
`...`	parameters for Rsubread::featureCounts.
`fullModel`	The full model formula
`reducedModel`	Null model formula.
`fitExpToVar`	A variable name contained in the sample data. The expression values will be fitted to this variable using the the formula " ~ sample + fitExpToVar * exon".
`drseq.fdr`	`numeric`, FDR (BH procedure) adjusted p-value cut-off.
`read.length`	`numeric`, RNA-seq read length. Default is 100 bp (e.g., Illumina TruSeq). This is used to adjust event base count, which is then used to select the representative events if replicated.
`min.adjMean`	`numeric`, adjusted event base mean threshold.
`filter.overlap.event`	`logical`, whether (default to `TRUE`) to select one representitive event from overlapping ones and remove the others.
`cores`	`integer`, number of available workers, sent to `nthreads` of `featureCounts`.
`verbose`	`logical`, whether (`TRUE`) to echo progress.

a surf object containing the DrSeq result in the drseqResults slot.

Chen, F., & Keles, S. (2020). SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins. Genome Biology, 21(1), 1-23.

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