quantifyExpressionsFromBWs: Evaluate introns and exons expressions from BAM or SAM files

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description

Given a TranscriptDb object and a list of bigWig (BW) files "quantifyExpressionsFormBWs" evaluates exons and introns expressions and the associated variances per each gene.

Usage

quantifyExpressionsFromBWs(
  txdb,
  BWfiles,
  experimentalDesign,
  readLength = 50,
  by = c("gene", "tx"),
  libsize = c("assigned", "all"),
  DESeq2 = TRUE,
  varSamplingCondition = NULL,
  BPPARAM = SerialParam()
)

Arguments

txdb	A TranscriptDB object
BWfiles	A vector of paths
experimentalDesign	A numerical which reports the desing of the experiment in terms of time points and replicates. Time points must be ordered according to the sequence of files submitted for the analysis, these labels characterize different files as replicates of a given condition.
readLength	A numerical that indicates the read length of the RNA-seq experiment. Used to normalize the coverage. By default, 50.
by	A character, either "gene" or "tx", indicating if expressions and counts should be summarized at the levels of genes or transcripts. "gene" by default. In case "tx" is selected, we suggest to set argument "allowMultiOverlap" to TRUE, otherwise the reads mapping to overlapping transcripts of the same gene will remain unassigned.
libsize	A character, either "assigned" or "all", indicating whether the libsize for expression normalization should include all mapped reads or only the reads assigned to any of the features. By default, "assigned" is selected.
DESeq2	A logical, if TRUE exons and introns variances are evaluated through the package DESeq2, if FALSE through plgem
varSamplingCondition	A character reporting which experimental condition should be used to sample the variance if DESeq2 = FALSE.
BPPARAM	Parallelization parameters for bplapply. By default SerialParam() By default, the first element of "experimentalDesign" with replicates.

Value

A list containing expressions and associated variances for exons and introns.

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.