Allele Specific Expression Quality Control.
This package has been authored by Kaushik Ganapathy and Eric Song.
To install this package:
- Clone this repository
- Load in the devtools library in R using
library(devtools) - Install the package using
devtools::install("path_to_cloned_repo")
Both refcounts and altcounts are R Dataframes with an index column and a column name containing the names of genes in addition to the columns for each sample. Ref counts will have the reference allele counts, and Alt counts will have the alternative allele counts from ASE Data.
The format is outlined below:
| name | sample 1 | sample 2 | ... | sample n | |
|---|---|---|---|---|---|
| 0 | Gene 1 | Count 1 | Count 2 | ... | Count n |
| 1 | Gene 2 | Count 3 | Count 4 | ... | Count m |
| ... | ... | ... | ... | ... | ... |
Both the index (unnamed) column and name column are essential for performing ASEQC fits.
The output file is an R dataframe with several columns. The std column indicates the ASEQC score, and the cutoff indicates the cutoff score above which samples are considered to fail the test.