loadOctadCounts: Load octad expression data

In Bin-Chen-Lab/octad: Open Cancer TherApeutic Discovery (OCTAD)

Load octad expression data

Description

Create TPM or count expression matrix for the selected samples from OCTAD.

Usage

  loadOctadCounts(sample_vector='',type='tpm',file='')

Arguments

sample_vector	vector of samples to be selected. Use phenoDF object for sample id selection.
type	either tpm (default) or counts to be returned.
file	full path to octad.counts.and.tpm.h5 file.

Value

exprData

matrix with either log2 corrected counts or tmp matrix for selected samples.

See Also

diffExp.

Examples

#load data.frame with samples included in the OCTAD database
phenoDF=get_ExperimentHub_data('EH7274') 
#load expression data for raw counts or tpm values.
HCC_primary=subset(phenoDF,cancer=='liver hepatocellular carcinoma'&
sample.type == 'primary') #select data
#case_id=HCC_primary$sample.id #select cases
#expression_tmp=loadOctadCounts(case_id,type='tpm',
#file='octad.counts.and.tpm.h5')
#expression_log2=loadOctadCounts(case_id,type='counts',
#file='octad.counts.and.tpm.h5')

Bin-Chen-Lab/octad documentation built on Jan. 28, 2023, 11:20 p.m.