Description Usage Arguments Value
Proccesses GTEx counts and merges counts statistics with classification data
1 2 3 4 | 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/")
|
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 |
dataframe with MAE/BAE classification and counts statistics
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