show_counts: Display all counts in a rectangular format

In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description

This function is for interactive purposes to inspect the read counts. The first column corresponds to feature id and all other columns correspond to read counts for each sample.

Usage

show_counts(x)

## Default S3 method:
show_counts(x)

## S3 method for class 'fpkm_counts'
show_counts(x)

## S3 method for class 'raw_counts'
show_counts(x)

Arguments

x	An object of class fpkm_counts or raw_counts. See ?gather_counts.

Value

An object of class data.table containing the feature and associated read counts for each sample in a tabular format.

See Also

rnaseq limma_dge edger_dge as.eset gather_counts construct_design construct_contrasts volcano_plot write_dge 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)
head(show_counts(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)
head(show_counts(raw_counts))

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