R/filter_features_by_FC.R

In leandroroser/RNASeqFunctions: Several functions for rna-seq analysis

#'Filter features by FC
#' @export

filter_features_by_FC <- function(x, group, delta = 1E-10,
                         threshold = 1,
                         as_cpm = TRUE, as_log = TRUE) {

summary_mat <- t(apply(x, 1, function(x) tapply(x, group, sum)))

if(as_cpm) {
summatry_mat <- normalize_counts_extra(summary_mat, "cpm")
}
combin <- combn(ncol(summary_mat), m = 2)

summary_mat <- summary_mat + delta
out <- list()
for( i in seq_len(ncol(combin))) {
  dat <- summary_mat[, combin[, i]]
  if(as_log) {
    dat <- log(dat[, 1], 2) - log(dat[, 2], 2)
  } else {
    dat <- dat[, 1] / dat[, 2]
  }
  out[[i]] <- dat
}

out <- do.call("cbind", out)
out <- abs(out)
good_features <- apply(apply(out, 1, function(x) x > threshold), 2, sum) != 0
cat(sum(!good_features ), " features filtered...\n")
list(counts = x[good_features , ], good_features = good_features)
}