Predict "important" time periods for a list of gene probes based on RNA-seq expression.
###Usage
genetime(genelist, thresh = 0.95, out.pdf = FALSE, out.name = "genetime.pdf", iters = 1000)
###Arguments
genelist A list of gene symbol identifiers
out.pdf output pdf of temporal enrichment patterns, defaults to FALSE. Default output name (set with out.name) is "genetime.pdf"
out.name name of output pdf of temporal enrichment patterns, default is "genetime.pdf"
iters Number of iterations for permutations to create null distributions, Default is 1000
threshold The quantile of expression values to take per gene. Default is 0.95
###Examples
mygenes = "ADNP" "AGAP2" "ANK2" "APH1A" thresh = 0.99 genelist(genelist=mygenes,threshold=thresh,out.pdf=TRUE,out.name="/home/myfile.pdf")
###Installation Since there is a data file over 100MB, it cannot be stored on github, so you must download them separately. First clone the repository
git clone https://github.com/vsoch/genetime mkdir genetime/data cd genetime/data
Download the data file
wget http://www.vbmis.com/bmi/data/interpolated_timeseries.rda
Change to the directory above the "genetime" folder, start R, and install from source
R install.packages("genetime",rep=NULL,type="source") library("genetime")