venkan
venkan
/ metadata_for_TCGA.r
Created
May 18, 2018 09:14
TCGA metadata - To get the read length, to check whether all the samples are paired-end and to get all other information for TCGA samples
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| library(GenomicDataCommons) | |
| q = files() %>% | |
| filter(~ cases.project.project_id == 'TCGA-LIHC' & | |
| data_type == 'Aligned Reads' & | |
| experimental_strategy == 'WXS' & | |
| data_format == 'BAM') %>% select('file_id') %>% | |
| expand('analysis.metadata.read_groups') | |
| file_ids = ids(q) | |
| z = results_all(q) | |
| read_length_list = sapply(z$analysis$metadata$read_groups,'[[','read_length') |
venkan
/ gtf_to_csv.R
Created
May 18, 2018 08:44
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| rm(list=ls()) | |
| library(GenomicFeatures) | |
| library(rtracklayer) | |
| extractGenesOfGTF <- function(inputFile, outputGTF_File, outputCsvFile ) { | |
| # reading the file. | |
| gtf <- import(inputFile) | |
| # its dimension is 2617197 by 25 | |
| gtf <- as.data.frame(gtf) |