jass_preprocessing.map_reference

Module of function

Functions

compute_is_aligned(mgwas)	Check if the reference panel and the GWAS data have the same reference allele.
compute_is_flipped(mgwas)	Check if the reference panel and the GWAS data have the same reference allele.
compute_snp_alignement(mgwas)	Add a column to mgwas indicating if the reference and coded allele is flipped compared to the reference panel. If it is, the sign of the statistic must be flipped :param mgwas: a pandas dataframe of the GWAS data merged with the reference panel.
map_on_ref_panel(gw_df, ref_panel[, index_type])	Merge Gwas dataframe with the reference panel Make sure that the same SNPs are in the reference panel and the gwas
read_reference(gwas_reference_panel[, ...])	helper function to name correctly the column :param gwas_reference_panel: path toward the reference panel file :type gwas_reference_panel: str :param mask_MHC: Whether the MHC region should be masked or not.