Parse RFMix MSP file

Source: R/ancestry_split.R

Parse the RFMix MSP (local ancestry tract) file into ancestry matrices. MSP format: two header lines followed by data rows. Line 1: population codes (e.g., "#Subpopulation order/codes: AFR=0 EUR=1"). Line 2: column headers. Data rows: ancestry calls per haplotype per tract.

.parse_msp(msp_path, verbose = TRUE)

Arguments

msp_path

Path to MSP file (plain text or gzipped).

verbose

Print progress messages.

Value

List with: pop_codes (named integer vector), sample_ids (character), tract_df (data.frame sorted by spos), anc_hap0 (integer matrix: samples x tracts), anc_hap1 (integer matrix: samples x tracts).