R/getChromStateRegression.R

In isglobal-brge/EASIER: EwAS: quality control, meta-analysIs and EnRichment

#' Significative variable Regression by cromatin state
#'
#' Get regression by cromatin state taking in to account a significative variable parameter like FDR values
#'
#' @param significative numerical. Variable to take in to account as significative variable, could be FDR, p-value,...
#' @param chromstate vector. Cromatin state values
#' @param varname string. Cromatin state name. For example : "TssA","TssAFlnk","TxFlnk","TxWk","Tx","EnhG","Enh","ZNF.Rpts","Het","TssBiv","BivFlnk","EnhBiv","ReprPC","ReprPCWk" or "Quies"
#' @filename
#'
#' @return
#'
#' @export
getChromStateRegression <- function(significative, chromstate, varname)
{
   rp <- as.data.frame.matrix(table(significative, chromstate))[,c("TRUE","FALSE")]

   rp1 <- rbind(nosig = rp[1, ], sig = colSums(rp[-1, ]))[c(2,1),]
   xt <- chisq.test(rp1)
   or <- (rp1[1, 1] * rp1[2, 2]) / (rp1[1, 2] * rp1[2, 1])

   return(list("ChromStates" = varname,
               "OR" = or,
               "OR.inf" = exp(log(or)-1.96*sqrt(sum(1/rp1))),
               "OR.sup" = exp(log(or)+1.96*sqrt(sum(1/rp1))),
               "p-val" = xt$p.value))
}