R/writeResTable.R

In PratheepaJ/diffTop: Differential topic analysis using latent Dirichlet allocation

#' Write differential topic analysis results to latex
#'
#' @param res A data frame. The results produced by DESeq2.
#' @param fileN String. A name for the file.
#'
#' @return A tex output will be saved with the filename.
#' @importFrom xtable xtable
#' @export
writeResTable <- function(res,
                          fileN = "fileName"
                          ){

  df <- data.frame(
    Topic = rownames(res),
    lfc = res$log2FoldChange,
    lfcSE= res$lfcSE,
    WTS = res$stat,
    pvalue = res$pvalue,
    p.adj = res$padj
    )
  df$lfc <- round(df$lfc, digits = 2)
  df$lfcSE <- round(df$lfcSE, digits = 2)
  df$WTS <- round(df$WTS, digits = 2)
  df$p.adj <- round(df$p.adj, digits = 4)
  df$p.adj[which(df$p.adj == 0)] <- "<.0001"
  print(xtable::xtable(df,
               type = "latex",
               digits = c(0,0,2, 2,2,2,4)),
        file = fileN)
}