R/misc.R

In luannnguyen/hmfGeneAnnotation: Determines gene amplifications and biallelic losses from HMF pipeline output

#' Miscellaneous functions

####################################################################################################
#' Write tsv file
#'
#' @param x The object to be written, preferably a matrix or data frame. If not, it is attempted to 
#' coerce x to a data frame.
#' @param file Path to the output file. If file ends with .gz, a gzip compressed file will be written
#' @param ... Arguments that can be passed to write.table()
#'
#' @return
#' @export
#'
write.tsv <- function(x, file, ...){
   write.table(
      x,
      if(grepl('[.]gz$',file)){ gzfile(file) } else { file },
      sep='\t', quote=F, row.names=F,
      ...
   )
}

####################################################################################################
#' Insert column(s) after a column of an existing dataframe
#'
#' @param df Input dataframe
#' @param v A vector or dataframe
#' @param after Column index or name
#' @param colname Set inserted column name. Has no effect if v is not a vector
#'
#' @return A dataframe with the inserted column(s)
#' @export
#'
insColAfter <- function(df, v, after, colname=NULL){
   if(is.character(after)){
      after <- which(colnames(df)==after)
   }

   df_l <- df[1:after]
   df_r <- df[(after+1):ncol(df)]

   df_new <- cbind(df_l, v, df_r)

   if(!is.null(colname)){
      colnames(df_new)[(after+1)] <- colname
   }

   return(df_new)
}