hmld {ldblock} | R Documentation |
import hapmap LD data and create a structure for its management
hmld(hmgztxt, poptag, chrom, genome = "hg19", stat = "Dprime")
hmgztxt |
name of gzipped text file as distributed
at
hapmap.ncbi.nlm.nih.gov/downloads/ld_data/2009-02_phaseIII_r2/.
It will be processed by |
poptag |
heuristic tag identifying population |
chrom |
heuristic tag for chromosome name |
genome |
genome tag |
stat |
statistic to use, "Dprime", "R2", and "LOD" are options |
generates a sparse matrix representation of pairwise LD statistics and binds metadata on variant name and position
instance of ldstruct class
getClass("ldstruct") # see vignette