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.