README.md
In lpwgit/sampleContamination: Sample Contamination R Package
R package for Sample Contamination Prediction
Purpose
Identify sample contamination base on variant allele frequency (VAF) detected from genome sequencing on tumor samples. An example of VAF data and its configuration file are distributed with this package under inst/extdata/. Refer method documentation here
Manual
Refer manual here
Installation
devtools::install_github("lpwgit/sampleContamination")
Example usage
library(sampleContamination)
data_path <- system.file('extdata',package='sampleContamination')
output_path <- 'output_express'
config_file <- system.file("extdata", 'config.txt', package = "sampleContamination", mustWork = TRUE)
run_sampleContamination(data_path = data_path,
output_path = output_path,
config_file = config_file)
lpwgit/sampleContamination documentation built on May 21, 2019, 7:51 a.m.
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R package for Sample Contamination Prediction
Purpose
Identify sample contamination base on variant allele frequency (VAF) detected from genome sequencing on tumor samples. An example of VAF data and its configuration file are distributed with this package under inst/extdata/. Refer method documentation here
Manual
Refer manual here
Installation
devtools::install_github("lpwgit/sampleContamination")
Example usage
library(sampleContamination) data_path <- system.file('extdata',package='sampleContamination') output_path <- 'output_express' config_file <- system.file("extdata", 'config.txt', package = "sampleContamination", mustWork = TRUE) run_sampleContamination(data_path = data_path, output_path = output_path, config_file = config_file)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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