startmitcr: Start MiTCR directly from the package.

In imminfo/tcr: Advanced Data Analysis of Immune Receptor Repertoires

Description

Start the MiTCR tools directly from the package with given settings.

Usage

startmitcr(
  .input = "",
  .output = "",
  ...,
  .file.path = "",
  .mitcr.path = "~/programs/",
  .mem = "4g"
)

Arguments

.input, .output	Input and output files.
...	Specify input and output files and arguments of the MITCR without first '-' to run it.
.file.path	Path prepending to .input and .output. If input and output is empty, but .file.path is specified, than process all files from the folder .file.path
.mitcr.path	Path to MiTCR .jar file.
.mem	Volume of memory available to MiTCR.

Details

Don't use spaces in paths! You should have insalled JDK 1.7 to make it works.

Examples

## Not run: 
# Equal to
# java -Xmx8g -jar ~/programs/mitcr.jar -pset flex 
#      -level 2 ~/data/raw/TwA1_B.fastq.gz ~/data/mitcr/TwA1_B.txt
startmitcr('raw/TwA1_B.fastq.gz', 'mitcr/TwA1_B.txt', .file.path = '~/data/',
  pset = 'flex', level = 1, 'debug', .mitcr.path = '~/programs/', .mem = '8g')

## End(Not run)

imminfo/tcr documentation built on June 13, 2020, 7:01 a.m.