as.dgelist: Convert to a 'DGEList' object

In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description

At the moment, these objects can be converted to a DGEList object directly by doing as.dgelist(x).

• fpkm_counts – object created by calling ganalyse::gather_counts on a fpkm object.

• raw_counts – object created by calling ganalyse::gather_counts on a raw object.

Usage

as.dgelist(x, ...)

## Default S3 method:
as.dgelist(x, ...)

## S3 method for class 'fpkm_counts'
as.dgelist(x, group = NULL, ...)

## S3 method for class 'raw_counts'
as.dgelist(x, group = NULL, ...)

Arguments

x	An object of class fpkm_counts or raw_counts.
...	Additional arguments specific to method.
group	column name in 'x' corresponding to the group each sample belongs to.

Details

The as.dgelist method is a simple wrapper for converting raw_counts and fpkm_counts objects to DGEList object. No additional transformations or filtering is done, i.e., it assumes that the counts are already filtered and (log) transformed as required. Use the arguments in gather_counts() method if necessary to prepare the counts as necessary.

Value

An object of class DGEList.

See Also

rnaseq, gather_counts show_counts limma_dge edger_dge construct_design construct_contrasts write_dge as.eset volcano_plot density_plot

Examples

path = system.file("tests", package="ganalyse")

# ----- fpkm ----- # 
fpkm_path = file.path(path, "fpkm", "annotation.txt")
fpkm_obj = rnaseq(fpkm_path, format="fpkm", experiment="sample")
fpkm_counts = gather_counts(fpkm_obj, by="gene-id", log_base=2L)
(as.dgelist(fpkm_counts))

# ----- raw ----- # 
raw_path = file.path(path, "raw", "annotation.txt")
raw_obj = rnaseq(raw_path, format="raw", experiment="sample")
raw_counts = gather_counts(raw_obj, by="gene-id", threshold=1L)
(as.dgelist(raw_counts))

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