geneWiseAnalysis: Downstream analysis of bundle-aggregated transcript abundance...

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

Description

Downstream analysis of bundle-aggregated transcript abundance estimates.

Usage

geneWiseAnalysis(kexp, design = NULL, how = c("cpm", "tpm"),
  p.cutoff = 0.05, fold.cutoff = 1, read.cutoff = 1,
  species = c("Homo.sapiens", "Mus.musculus"), fitOnly = FALSE,
  adjustBy = "holm")

Arguments

kexp	a KallistoExperiment or SummarizedExperiment-like object
design	a design matrix with 2nd coefficient as one to test
how	a character selection of tpm or cpm
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)
read.cutoff	minimum read coverage (estimated) for a gene bundle
species	which species? (Homo.sapiens, Mus.musculus are two currently supported
fitOnly	exit after fitting the EBayes linear model? (FALSE)
adjustBy	character none, BH,BY, or holm for FDR procedures

Details

If no design matrix is found, the function will look in metadata(kexp)$design. If that too is empty it fails.

Value

a list w/items design, voomed, fit, top, enriched, Figures, scaledExprs, clusts, species, features, ... (perhaps)

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