Defines functions pSI.count

Documented in pSI.count

#'Convert pSI output to gene count list
#'\code{pSI.count} This functions counts number of genes specific to each sample type
#'Returns data frame consisting of 6 rows, one for each pSI threshold, and as many columns as cell types/samples were included in the analysis.
#'Each cell type/sample will have a count of many genes whose pSI values fall below each respective threshold for each cell type/sample.
#'NOTE:Supplementary data (human & mouse expression sets, calculated pSI datasets, etc.) can be found in \code{pSI.data} package located at the following URL:
#'@param pSIs  data frame output from \code{specificity.index} function with the number of columns equal to the number of samples and genes as rows.
#'@param write.csv logical variable indicating if csv files will be written to the current working directory (default value is FALSE)
#'@author Xiaoxiao Xu, Alan B. Wells, David OBrien, Arye Nehorai, Joseph D. Dougherty
#'##load sample pSI output
#'##Count the number of genes specific to each cell type/sample type across all pSI thresholds
#'pSI.out.count <- pSI.count(pSIs=sample.data$pSI.output, write.csv=TRUE)

pSI.count <- function(pSIs, write.csv=FALSE){
  #Assigning variables used in loop, ie number of genes, number of samples etc.
  gene_l <- length(pSIs[,1])
  samples <- pSIs[1,]
  n_samples <- length(pSIs[1,])
  #name_columns <- c(seq(from=1, to=ncol(pSIs), by=2))
  names <- data.frame(array(NA, dim=c(1,n_samples)))
  names<- colnames(pSIs)
  for(b in c(0.05, 0.01, 0.001, 0.0001)){
    #create data frame to hold gene counts
    gene_count <- data.frame(array(NA, dim=c(1,1)))
    for(i in 1:n_samples){
      #filter out all NA values, then count how many fall below the current threshold for a given cell type 
      sig_tmp <- pSIs[!is.na(pSIs[,i]),]
      sig_tmp <- sig_tmp[sig_tmp[,i] < b,]
      gene_count <- cbind(gene_count, length(sig_tmp[,i]))
    #during the first iteration of the previous loop the gene_count data set is column bound onto itself and must be removed
    gene_count <- gene_count[-1]
    #Assigns descriptive name to temporary loop variable
    assign(paste("gene_count", b, sep="_"),gene_count)
  #row bind all the different and assign row & column names
  gene_count_1 <- rbind(get("gene_count_1e-04"), get("gene_count_0.001"), get("gene_count_0.01"), get("gene_count_0.05"))
  rownames(gene_count_1) <- c("0.0001", "0.001", "0.01", "0.05")
  colnames(gene_count_1) <- colnames(pSIs)
  #if boolean for writing CSV is TRUE then file will be written in current working directory

Try the pSI package in your browser

Any scripts or data that you put into this service are public.

pSI documentation built on May 1, 2019, 10:28 p.m.