slowkow

#' Convert counts to transcripts per million (TPM).
#' 
#' Convert a numeric matrix of features (rows) and conditions (columns) with
#' raw feature counts to transcripts per million.
#' 
#'    Lior Pachter. Models for transcript quantification from RNA-Seq.
#'    arXiv:1104.3889v2 
#'    
#'    Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
#'    RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.

slowkow

# RPKM versus TPM
# 
# RPKM and TPM are both normalized for library size and gene length.
#
# RPKM is not comparable across different samples.
#
# For more details, see: http://blog.nextgenetics.net/?e=51

rpkm <- function(counts, lengths) {
  rate <- counts / lengths 

decodebiology

# This R script is to generate the TF or histone modification heatmap
# at certain genomic features (TSS, enhancers) from the ChIP-seq data
# the input matrix is got from Homer software. alternative to R, use cluster3 to cluster, and visualize by # java Treeviewer
# generate the matrix by Homer: annotatePeaks.pl peak_file.txt hg19 -size 6000 -hist 10  -ghist -d TF1/ # > outputfile_matrix.txt
# see several posts for heatmap:
# http://davetang.org/muse/2010/12/06/making-a-heatmap-with-r/
# http://www.r-bloggers.com/r-using-rcolorbrewer-to-colour-your-figures-in-r/
# 08/20/13 by Tommy Tang

# it is such a simple script but took me several days to get it work...I mean the desired