read¶

craft.read.abf_cred(file)[source]¶: Read CRAFT .abf.cred file into a dataframe.

craft.read.annovar(file, file_exonic, colnames)[source]¶

Read ANNOVAR output files into an internal dataframe.

Gene annotation with ANNOVAR returns two different output files (variant_function and exonic_variant_function).

Where exonic SNPs exist, we merge the additional data of exonic variant function, and genes + transcript ID + protein-level change into the dataframe based on matching rsids.

craft.read.cred_annotated(file)[source]¶: Read CRAFT .cred.annotated file into a dataframe.

craft.read.csv(file)[source]¶: Read csv data into an internal dataframe.

craft.read.finemap_cred(file)[source]¶: Read FINEMAP .cred file into a dataframe.

craft.read.index(file)[source]¶: Read CRAFT .index output file into a dataframe.

craft.read.ld(file)[source]¶: Read CRAFT .ld output file into a numpy array.

craft.read.maps(source_dir)[source]¶: Read genetic map data into a maps object.

craft.read.plink(file, frq_file)[source]¶: Read plink (.assoc.logistic) data into an internal dataframe.

craft.read.snp(file)[source]¶: Read FINEMAP .snp file into a dataframe.

craft.read.snptest(file)[source]¶: Read snptest data into an internal dataframe.

craft.read.variant_file(file)[source]¶: Read CRAFT variant_file rsids into a list.