as.eset: Convert objects to an 'ExpressionSet' object

Description Usage Arguments Value See Also Examples

Description

At the moment, these objects can be converted to an ExpressionSet object directly by doing as.eset(x).

Usage

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as.eset(x, ...)

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

## S3 method for class 'DGEList'
as.eset(x, groups = NULL, ...)

## S3 method for class 'fpkm_counts'
as.eset(x, groups = NULL, ...)

## S3 method for class 'raw_counts'
as.eset(x, groups = NULL, ...)

Arguments

x

An object of class fpkm_format, raw_format or DGEList.

...

Additional arguments specific to methods.

groups

columns in 'x' corresponding to the group each sample belongs to.

Value

An object of class ExpressionSet.

See Also

rnaseq, gather_counts show_counts limma_dge edger_dge construct_design construct_contrasts write_dge as.dgelist 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.eset(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.eset(raw_counts))

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