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

In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description

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

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

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

• DGEList – object created by calling edgeR::DGEList function.

Usage

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

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.