franktwen / meso-lymph

meso-lymph

This repo contains scripts for naming genes from ExomeDepth outputs.

ExomeDepth outputs are placed in data. The script scripts/name_genes.R gets gene names from Ensembl using the the R biomaRt package and merges them with the ExomeDepth output files. The named output files are written to outputs. The output files contain the following new columns:

hgnc_symbol gene name

start_gene gene starting point from ensembl

end_gene gene ending point from ensembl

start_intersect used for merging data based on coordinates

end_intersect used for merging data based on coordinates

filename the name of the file

rowId a unique row indicator for each row in the original ExomeDepth file (e.g. 1-10000 for each file)

Note that unnamed reads are not included in the output.

How to run the name_genes.R script

1. put all the exomeDepth outputs into the data directory
2. open and run the name_genes.R script