createRSEDS: create a RangedSummarizedExperiment from a RNAseq count table...

In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

create a RangedSummarizedExperiment from a RNAseq count table and a phenotypes table

Description

create a RangedSummarizedExperiment from a RNAseq count table and a phenotypes table

Usage

createRSEDS(rnaseq, phe, ...)

Arguments

rnaseq	data.frame RNAseq count table
phe	data.frame Phenotypes table
...	character vector Columns of the counts table to be used as annotation when creating the SummarizedExperiment. If NULL, biomaRt will be used to find annotation using the first column of the counts table (EntrezID)

Details

The RNAseq count table has to have the following structure:
- First column: Entrez identificator (column named "EntrezID")
- Second column: Annotated symbol (optional, but if present must be on this position, if not present, make sure to set annot = FALSE)
- All the remaining columns: One col. per individual
The phenotypes table has to have the following structure:
- First column: ID of the individuals. To match with the column names of the RNAseq table
- All the remaining columns: One col. per phenotype

Value

A RangedSummarizedExperiment object

isglobal-brge/dsOmics documentation built on March 22, 2023, 4:01 a.m.