comparePCBeforeAfterPrePro: Visualize PCA before and after preprocessing expression...

In holgerman/HT12ProcessoR: Preprocessing Illuminas HT12 v4 data

Description

PCA on expression data is done using good samples surviving preprocessing. Following PCAs are calculated and shown as figures: PCA of all transcripts before preprocessing, including additional scaling, PCA of gene expression after preprocessing using only expression probes that are expressed, not overinflated regarding batch affects and beeing specific to the human genome when considering a remapping approach according to Barbosa-Moralis et al. (2010)

Usage

comparePCBeforeAfterPrePro(ht12object, paramfile = NULL, showPlots = T)

Arguments

ht12object	A list object of class HT12prepro created with function visualizePreprocessing
paramfile	Path to the file specifying parameters

Value

A list object of class HT12prepro including updated slots, e.g the slot with the history of the commands named '$history“ is updated. Plots are also stored in slot '$'

holgerman/HT12ProcessoR documentation built on Sept. 6, 2018, 1:54 p.m.