process_to_counts: Proccesses GTEx counts and merges counts statistics with...

In kintany/GTExR: Package for GTEx analysis with R scripts

Description

Proccesses GTEx counts and merges counts statistics with classification data

Usage

process_to_counts(name, keepCounts = FALSE, sample_names = "all",
  mode = "norm_counts",
  path_to_class = "/Users/svetlana/Dropbox (Partners HealthCare)/variation_project/GTEx/GTExR/data/classification/",
  path_rda = "/Users/svetlana/Dropbox (Partners HealthCare)/variation_project/GTEx/GTExR/data/data_Rda/")

Arguments

name	Tissue name
keepCounts	Keep columns with counts in the output
sample_names	Default is set to all meaning "all samples"; can be a string of names (c("GTEX-111CU-1326-SM-5NQ8L", "GTEX-111YS-1426-SM-5GID8", "GTEX-1122O-1326-SM-5H11F"))
mode	"norm_counts" / "log" meaning using normalized by library size counts or using log(normalized_counts)
path_to_class	Path to file name_class.txt with MAE/BAE classification call (output by MAGIC or RNA-seq analysis)
path_rda	Path to the folder contatining all .Rda files for tissues

Value

dataframe with MAE/BAE classification and counts statistics

kintany/GTExR documentation built on May 14, 2019, 7:36 a.m.