R/testPattern.R

In pcahan1/cancerCellNet: CellNet, for cancer

#' @title
#' Template Matching
#'
#' @description
#' Match the template created \code{\link{sc_sampR_to_pattern}} with expression data
#'
#' @param pattern the template pattern created from \code{\link{sc_sampR_to_pattern}}
#' @param expDat normalized expression data
#'
#' @return a dataframe of genes with pval, cval and holms
#' @export
sc_testPattern<-function(pattern, expDat){
  pval = vector()
  cval = vector()

  geneids = rownames(expDat)  # get the gene names of the exp matrix

  llfit = ls.print(lsfit(pattern, t(expDat)), digits=25, print=FALSE)

  pos_R_index = which(as.numeric(llfit$summary[,2]) >= 0) # R-squared value

  xxx = matrix(unlist(llfit$coef), ncol=8,byrow=TRUE)

  ccorr = xxx[pos_R_index,6]  # t-value of X coefficient
  cval =  sqrt(as.numeric(llfit$summary[pos_R_index,2])) * sign(ccorr)  # R squared

  pval = as.numeric(xxx[,8])  # p-value of X coefficient
  holm = p.adjust(pval, method='holm')


  return(data.frame(row.names=geneids[pos_R_index], pval=pval[pos_R_index], cval=cval,holm=holm[pos_R_index]))
}