GSProcess: Process the tables produced by GenomeStudio and saved in the...

In buddha2490/BERGgeneQC: Processing GenomeStudio output in the BERG

Description

GenomeStudio will produce three sets of tables: The Samples table, SNP table, and FullData tables. Each of these has a piece of data we will need. This function will process all the output files.

Usage

GSProcess(home)

Arguments

home	Home file path for the projects.

Details

This function can take quite a while to run, probably about half an hour to an hour for a batch of 96 samples. In order to reduce the total run time, the function will search for previously completed projects in the directories so that they are not rerun.

Value

Three sets of RDS files are saved in the "Processed Files" folder:

Samples_...RDS - sample summary file for each of the samples in the batch

SNPTable_...RDS - SNP summary statistics for the batch.

FullDataTable...RDS - Additional SNP statistics by batch.

This also saves the BAF/LRR statistics for each sample. Each sample recieves a single file and is saved at "~/BAF/Files"

Author(s)

Brian Carter

Examples

src <- file.path("s:/diet validation genotyping")
GSProcess(src)

buddha2490/BERGgeneQC documentation built on Feb. 18, 2020, 9:35 p.m.