RNAseq.data4Tyers: Generate a data frame with the data4Tyers format from RNAseq...

Description Usage Arguments Details Value Author(s)

View source: R/RNAseq.data4Tyers.R

Description

Generate a data frame with the data4Tyers format to run the macro in excel.

Usage

1
RNAseq.data4Tyers(expr.mat, annot.mat, cond, fit.main, contrast, specie="human", GOndKEGG=TRUE)

Arguments

expr.mat

Matrix with expression values in CPM (E object provided by voom), TMM or counts with rownames equal to the "Geneid"" column in annot.mat.

annot.mat

Matrix with annotations obtained with featurecounts function in subread package it has to have a column with gene symbols named "Geneid".

cond

Vector with sample conditions used in the contrasts, sample order with same order as colnames(expr.mat).

fit.main

Model to use in limma analysis.

contrast

List of vectors with each contrast to use.

specie

Specie used to make annotations (human or mouse). It is required when using the option GOndKEGG=TRUE.

GOndKEGG

TRUE if we want to make KEGG and GO annotations for genes.

Details

Build a data frame with the columns required to run the macro data4Tyers. This data frame contains information regarding gene anotation, statistics of the analysis and expression values (normalized or not) of RNAseq data.

Value

data.frame object

Author(s)

Magdalena Arnal Segura <marnal@imim.es>


machalen/AnalysisFunctions documentation built on Nov. 11, 2019, 10:26 a.m.