cgdata.core

detect-cgdata

(detect-cgdata file)
Detect cgdata files by presence of json metadata. If no type
is given, assume genomicMatrix

detect-tsv

(detect-tsv file)
Return ::tsv if the file is tsv, or nil

fix-json

(fix-json root)
Utility for rewriting references in cgdata metadata, so
they refer to file paths, not abstract identifiers.

gene-pred-file

(gene-pred-file file & {docroot :docroot, :or {docroot fs/unix-root}})
Return a map describing a genePred(Ext) file. This will read
any assoicated json.

matrix-file

(matrix-file file & {docroot :docroot, :or {docroot fs/unix-root}})
Return a map describing a cgData matrix file. This will read
any assoicated json or clinicalFeature file.

mutation-file

(mutation-file file & {docroot :docroot, :or {docroot fs/unix-root}})
Return a map describing a cgData mutation file. This will read
any assoicated json.

probemap-file

(probemap-file file & {docroot :docroot, :or {docroot fs/unix-root}})
Return a map describing a cgData probemap file. This will read
any assoicated json.