transcriptWiseAnalysis: Analysis of raw transcript abundance estimates.

In RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

Description

Analysis of raw transcript abundance estimates.

Usage

transcriptWiseAnalysis(kexp, design, p.cutoff = 0.05, fold.cutoff = 1,
  coef = 2, read.cutoff = 1, tx_biotype = NULL, gene_biotype = NULL,
  biotype_class = NULL, adjustBy = "holm", species = c("Homo.sapiens",
  "Mus.musculus"))

Arguments

kexp	a KallistoExperiment or SummarizedExperiment-like object
design	a design matrix w/contrast or coefficient to test in col2
p.cutoff	where to set the p-value cutoff for plots, etc. (0.05)
fold.cutoff	where to set the log2-FC cutoff for plots, etc. (1 == 2x)
coef	which column of the design matrix to test on (2nd)
read.cutoff	a cutoff to filter reads below across samples
tx_biotype	optionally restrict to one or more tx_biotype classes
gene_biotype	optionally restrict to one or more gene_biotype classes
biotype_class	optionally restrict to one or more biotype_class ...es
adjustBy	either none , BH, BY, holm for limma adjust type
species	character , either Homo.sapiens or Mus.musculus

RamsinghLab/arkas_staging documentation built on March 14, 2021, 11:40 a.m.