crossModels: Often times it is needed to cross compare edgeR results,...

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

Description

Often times it is needed to cross compare edgeR results, limma/voom results across various filtering criteria and comparing normalized results and unnormalized results, comparing gene-level, and / or transcript level at various filtering criteria reproducibly. This function can run a cross model generation set across various filtering criteria. by default the design is a treatment factorization where the coeficient is the second column with an intercept term.

Usage

crossModels(kexp, crossLevel = c("tx_id", "gene_id"), cutoffMax = 3,
  dataType = c("normalized", "unnormalized"), outputDir = ".",
  design = NULL, setP = 0.05, adjustBy = "BH",
  species = c("Homo.sapiens", "Mus.musculus"), numberSelected = 200,
  saveReport = FALSE)

Arguments

kexp	a kalistoExperiemtn of something of this sort
crossLevel	character option of tx_id, or gene_id which will compare at the transcript or gene level collapse.
cutoffMax	integer, this will be the maximum read.cutoff that will compare each read.cutoff up to the max, i.e. from 1<=cutoffMax thresholding.
dataType	character either normalized or unnormalized data to compare. if normalized is selected, then ruv is ran to only compare across normalized results.
outputDir	a character path to save all the pdfs printed, includes limma volcano plots, heatmaps.
design	a matrix with a treatment level contrasts, does not yet support group-means factorization
setP	numeric for linear fitting
adjustBy	character either BH,none,BY,holm
species	character Homo.sapiens or Mus.musculus
numberSelected	integer, this is the number of the highest ranked adj.P.Val genes to print into a heatmap, the max amount is the number of genes returned from an analysis.
saveReport	boolean, if true then a txt and csv files are printed out to file, if false, then no report is printed out

Value

returns several images plotted.

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