dot-prep_illumina_headers: Prep Illumina Headers

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

Prep Illumina Headers

Description

For read.ilmn() to work correctly the signal cols need format <smpl>.<exprValTerm> with the expression-value term being something like "AVG_Signal" or "SAMPLE". Then the detection p-value cols must have format <smpl>.Detection Pval. This way the rawElist creates the $E and $other$Detection matrices with same colnames of <smpl>. Since in this script the read.ilmn(file, exprs = "AVG_Signal", probeid = "ID_REF) is hardcoded. The vars are substituted here for other viable versions, e.g. SAMPLE and PROBE_ID.

Usage

.prep_illumina_headers(raw_illumina_dt)

Arguments

raw_illumina_dt

data.table of raw illumina values.

Value

data.table with cleaned up names ready for read.ilmn()

RGLab/HIPCMatrix documentation built on Jan. 29, 2023, 5:13 a.m.