rglimpse2_genetic_map() resolves one absolute installed map path.
rglimpse2_genetic_maps() returns the complete packaged inventory. The
autosomal and chromosome X files are byte-identical copies from the pinned
GLIMPSE source tree. The Y non-PAR and mitochondrial files are derived
two-anchor, zero-recombination coordinate maps, not empirical maps.
Usage
rglimpse2_genetic_maps()
rglimpse2_genetic_map(assembly = "GRCh38", chromosome, region = character())Arguments
- assembly
Reference assembly, either
"GRCh37"or"GRCh38".- chromosome
One autosome named
"1"through"22","X","Y", or"MT". A leading"chr"is accepted. Mitochondrial aliases"M","MT","chrM", and"chrMT"all resolve to the same map.- region
Empty to select the chromosome default, or one of
"full","nonpar","par1", or"par2". The default is"nonpar"for X and Y and"full"otherwise.
Value
rglimpse2_genetic_map() returns one absolute file path.
rglimpse2_genetic_maps() returns a data frame describing every map and
its absolute installed path.
Examples
rglimpse2_genetic_map("GRCh38", "22")
#> [1] "/home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b38/chr22.b38.gmap.gz"
rglimpse2_genetic_map("GRCh37", "Y")
#> [1] "/home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chrY_nonpar.b37.gmap.gz"
rglimpse2_genetic_map("GRCh38", "Y")
#> [1] "/home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b38/chrY_nonpar.b38.gmap.gz"
rglimpse2_genetic_map("GRCh37", "chrM")
#> [1] "/home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chrMT.b37.gmap.gz"
rglimpse2_genetic_map("GRCh38", "MT")
#> [1] "/home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b38/chrMT.b38.gmap.gz"
head(rglimpse2_genetic_maps())
#> assembly chromosome region kind start_bp end_bp start_cm end_cm
#> 1 GRCh37 1 full empirical 55550 249218992 0 286.2792
#> 2 GRCh37 2 full empirical 12994 243090997 0 268.8396
#> 3 GRCh37 3 full empirical 61113 197874528 0 223.3611
#> 4 GRCh37 4 full empirical 12906 191028645 0 214.6885
#> 5 GRCh37 5 full empirical 20583 180715810 0 204.0894
#> 6 GRCh37 6 full empirical 92012 171051316 0 192.0399
#> entries file source
#> 1 256895 genetic_maps.b37/chr1.b37.gmap.gz GLIMPSE-pinned-upstream
#> 2 286355 genetic_maps.b37/chr2.b37.gmap.gz GLIMPSE-pinned-upstream
#> 3 223360 genetic_maps.b37/chr3.b37.gmap.gz GLIMPSE-pinned-upstream
#> 4 211115 genetic_maps.b37/chr4.b37.gmap.gz GLIMPSE-pinned-upstream
#> 5 215414 genetic_maps.b37/chr5.b37.gmap.gz GLIMPSE-pinned-upstream
#> 6 234422 genetic_maps.b37/chr6.b37.gmap.gz GLIMPSE-pinned-upstream
#> md5
#> 1 15f098ee8a9f803657608559eef3bc2a
#> 2 20b2a865e5d04daf5d0c5422934bf1ac
#> 3 53e7da0e5a2f4bb96007fd57f46dfa4d
#> 4 ff22f04a9120ae90a185f6926b7ff4bf
#> 5 c04e073550d715ce52ae35070b241080
#> 6 4d30099024d5f233002d06452a02f1f0
#> path
#> 1 /home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chr1.b37.gmap.gz
#> 2 /home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chr2.b37.gmap.gz
#> 3 /home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chr3.b37.gmap.gz
#> 4 /home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chr4.b37.gmap.gz
#> 5 /home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chr5.b37.gmap.gz
#> 6 /home/runner/work/_temp/Library/RGlimpse2/genetic_maps/genetic_maps.b37/chr6.b37.gmap.gz