get_sumabsdsg: For each individual, summarize loci infomation (DSGsum,...

In huanglu2018/tSTR: functions used in gtex2str project

Description

For each individual, summarize loci infomation (DSGsum, DSGmean, DPsum, DPmean, absDSGsum, absDSGmean) by groups of loci defined by loci_list

Usage

get_sumabsdsg(mydir, loci_list)

Arguments

mydir	dir containning .vcfs created by gangSTR
loci_list	a list containing groups of loci

Value

dataframe with summarized information example:

sample eachdis DSGsum DSGmean DPsum DPmean absDSGsum absDSGmean norm_dsg norm_absdsg 2 SRR2155717.vcf 1 334 0.878947368421053 16588 43.6526315789474 766 2.0157895 0.0201350374 0.04617796 3 SRR2155717.vcf 2 -70 -0.171990171990172 18435 45.2948402948403 490 1.2039312 -0.0037971250 0.02657988 4 SRR2155717.vcf 3 23 0.0484210526315789 21917 46.1410526315789 473 0.9957895 0.0010494137 0.02158142 5 SRR2155717.vcf 4 25 0.0389408099688473 28709 44.7180685358255 491 0.7647975 0.0008708071 0.01710265 6 SRR2155717.vcf 5 77 0.133913043478261 26145 45.4695652173913 629 1.0939130 0.0029451138 0.02405814

Examples

loci_list example as defined by exon boundary distance:

[[1]]
[1] "chr1__6931916"    "chr1__10718732"   "chr1__25757550"   "chr1__31666544"   "chr1__32739601"

[[2]]
[1] "chr1__36032231"   "chr1__40255942"   "chr1__40713708"   "chr1__42094312"

huanglu2018/tSTR documentation built on Feb. 25, 2022, 5:39 a.m.