R/filter_by_pos.R

In kkdey/aRchaic.site: Visualization, Exploration and Clustering of Ancient vs Modern BAM mutation patterns

####################   filter by pos   #################################

filter_by_pos <- function(mat, max_pos = 20){
  input_pos <- 1:max_pos
  pos <- as.numeric(sapply(as.character(colnames(mat)), function(x) return (tail(strsplit(x,"_")[[1]],1))))
  pos_indices <- which(!is.na(match(pos, input_pos)))
  pos_reduced <- pos[pos_indices]

  mat_reduced <- mat[,pos_indices]
  mat_filtered <- as.numeric()
  for(l in 1:dim(mat)[1]){
    mat_filtered <- rbind(mat_filtered, tapply(mat_reduced[l,], pos_reduced, sum))
  }
  rownames(mat_filtered) <- rownames(mat)

  return(mat_filtered)
}