R/loadOctadCounts.R

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

#' @export
#' @import rhdf5
#### runsRGES #######
loadOctadCounts <- function(sample_vector='',type='tpm',file=''){
    #    require(dplyr)
    #    require(RUVSeq)
    transcripts = as.character(rhdf5::h5read(file, "meta/transcripts"))
    samples = as.character(rhdf5::h5read(file, "meta/samples"))
    if(type=='counts'){
        
        #print(paste('loading samples from whole OCTAD dataset log2 values for',length(sample_vector),'samples',sep=' '))
        print(paste('loading',length(transcripts),'log2 expression values for',length(sample_vector),'samples',sep=' '))
        
        exprData = rhdf5::h5read(file, "data/count", index=list(1:length(transcripts), which(samples %in% sample_vector)))
        rownames(exprData) = transcripts
        colnames(exprData) = samples[samples %in% sample_vector]
        rhdf5::H5close()
        return(exprData)
    }else if(type=='tpm'){
        
#        rownames(exprData) = transcripts
        print(paste('loading',length(transcripts),'TPM expression values for',length(sample_vector),'samples',sep=' '))
        
        exprData = rhdf5::h5read(file, "data/tpm", index=list(1:length(transcripts), which(samples %in% sample_vector)))
        rownames(exprData) = transcripts
        colnames(exprData) = samples[samples %in% sample_vector]
        
        rhdf5::H5close()
        return(exprData)
        #}else if(source=='octad.small'&type=='counts'){
        
        #print(paste('loading small OCTAD set containing only log2 expression values for 978 LINCS genes for',length(sample_vector),'samples',sep=' '))
        
        #exprData = rhdf5::h5read(file, "data/count", index=list(1:length(transcripts), which(samples %in% sample_vector)))
        #colnames(exprData) = samples[samples %in% sample_vector]
        #rownames(exprData) = transcripts
        #rhdf5::H5close()
        #return(exprData)
        #}else if(source=='octad.small'&type=='tpm'){
        
        #print(paste('loading small OCTAD set containing only TPM expression values for 978 LINCS genes for',length(sample_vector),'samples',sep=' '))
        
        #exprData = rhdf5::h5read(file, "data/tpm", index=list(1:length(transcripts), which(samples %in% sample_vector)))
        #colnames(exprData) = samples[samples %in% sample_vector]
        #rownames(exprData) = transcripts
        #rhdf5::H5close()
        #return(exprData)
    }else{
        print('Oops, some parameters are missing, check everything is ok and restart function')}
    rhdf5::H5close()
}