ds.createRSE: Create a RangedSummarizedExperiment from a RNAseq count table...

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association 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

ds.createRSE(
  rnaseq,
  phe,
  annotCols = NULL,
  newobj.name = NULL,
  datasources = NULL
)

Arguments

rnaseq	character Name of the RNAseq table on the server
phe	character Name of the phenotypes table on the server
annotCols	character vector (default NULL) 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)
newobj.name	character (default NULL) Name to be assigned on the server to the RangedSummarizedExperiment. If NULL the created RSE will be assigned to a variable named 'RSE'
datasources	a list of DSConnection-class (default NULL) objects obtained after login

Details

The RNAseq count table has to have the following structure:
- First column: Entrez identificator
- All the remaining columns: One col. per individual + annotation columns (no special order required, they can even be mixed)
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

This function does not have an output. It creates (or overwrites) a data frame on the study server.

isglobal-brge/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.