as.dgelist: Convert to a 'DGEList' object

Description Usage Arguments Details Value See Also Examples

Description

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

Usage

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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

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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.