| Class | Data Declaration command |
| Name | read locus linkage |
| Arguments | <locus file name> <locus_column_name> <chromosome_column_name> <base_pair_position_column_name> [<refall_column_name> <altall_column_name>] [human] |
Read locus names, types and map positions from a rectangular locus (.map) file where the first line contains names for each column. The column names corresponding to the locus name, chromosome, map position (bp), and referance and alternate alleles are specified as arguments. These can be numeric if names are not provided.
Example:
>> head top10k.dat CHR BP SNP A1 A2 EAF BETA SE P 11 30226356 11:30226356 t c 0.8562 0.1564 0.0161 2.169e-22 11 30226528 11:30226528 a g 0.1439 -0.156 0.016 2.37e-22 11 30242287 11:30242287 t c 0.8368 0.1453 0.0153 1.577e-21 11 30339461 11:30339461 a g 0.8366 0.1449 0.0152 1.794e-21 >> read locus file top10k.dat SNP CHR BP A1 A2 human Locus name : "SNP". Chromosome : "CHR". Map position : "BP". Ref allele : "A1". Alt allele : "A2". Read in names of 10000 loci from "top10k.dat". >> read chain ~/Genetics/Maps/hg19ToHg38.over.chain.gz Reading chain file "/home/davidD/Genetics/Maps/hg19ToHg38.over.chain.gz". Lifted over 10000 (100.0%) map positions.
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