as.eset_map: Detailed 'ExpressionSet' object

In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description

as.eset_map() converts an object of class fpkm_counts or raw_counts to an ExpressionSet object, with a lot of other details that are normally required for DGE analysis, but might be necessary at times.

This function is still in development, hence not exported.

Usage

as.eset_map(x, entrez_map = NULL, reference_group = "", ...)

## Default S3 method:
as.eset_map(x, entrez_map = NULL, ...)

## S3 method for class 'fpkm_counts'
as.eset_map(x, entrez_map = NULL, genome_annotation,
  gene_name_col, reference_group = "", ...)

## S3 method for class 'raw_counts'
as.eset_map(x, entrez_map = NULL, genome_annotation,
  gene_name_col, reference_group = "", ...)

Arguments

x	An object of class fpkm_counts, raw_counts or DGEList.
entrez_map	Full path to file that contains mapping of gene names to ENTREZ ids along with corresponding gene ids . It must be a three column data.table, with column names gene_name, entrez_id and gene_id respectively. If the argument is NULL (default), the column ENTREZID in object pData(featureData(<eset_obj>)) will be set to NA.
reference_group	A character vector of length=1 indicating the reference sample.
...	Additional arguments specific to methods.
genome_annotation	An object of class gtf or gff.
gene_name_col	A character vector of length=1 indicating the name of the column corresponding to gene names in genome_annotation

Value

An object of class ExpressionSet tuned for MAP.

Examples

## Not run: 
  # my_gtf is obtained using gread::read_format.
  eset_obj = as.eset_map(x, genome_annotation = my_gtf, 
                   gene_name_col = "gene_name")

## End(Not run)

openanalytics/ganalyse documentation built on May 24, 2019, 2:25 p.m.