save_to_file: Save the tibble defining feature ranges to a tab-delimited...

In UW-GAC/genetable: Functions to Build a Gene Definitions Table in the GAC Database

Description

Save the tibble of genomic feature ranges to a tab-delimited file with appropriate header columns.

Usage

save_to_file(feature_bounds, file_name, notes)

Arguments

feature_bounds	a tibble such as produced by define_boundaries()
file_name	the target file name for writing (default "feature_bounds_DATE.tsv")
notes	a character string of notes to include in the file header.

Details

The output file includes the following fields as comments in the header: Date: $DATE genetable Version: $VERSION Notes: $NOTES Data Dictionary: variable type description chr character chromosome in genome build GRCh37/hg19 start integer 5' start position of the gene in genome build GRCh37/hg19 end integer 3' end position of the gene in genome build GRCh37/hg19 strand character DNA strand. values +,- gene_id character gene identifier with ENSG prefix gene_name character Gene name type character biotype of the feature

Examples

## Not run: 
notes <- paste("Features selected by filtering gtf for feature =",
               '"transcript" and tag = "basic"', sep = " ")
save_to_file(gene_bounds, file_name = "gene_bounds_20170504", 
             notes = notes)

## End(Not run)

UW-GAC/genetable documentation built on May 5, 2019, 11:08 p.m.