str_somatic_vs_germline: used to analysis the str profile, compare them to the...

In huanglu2018/tSTR: functions used in gtex2str project

Description

used to analysis the str profile, compare them to the correspinding germline profile

Usage

str_somatic_vs_germline(RNAseq_GT, WGS_GT)

Arguments

RNAseq_GT	result of tSTR::vcf2GT() and tSTR::get_correspond_sample_info()
WGS_GT	result of tSTR::vcf2GT() and tSTR::get_correspond_sample_info()

Value

a dataframe include columns:loci T_gt_GT,TG1,TG2,T_REF,G_gt_GT,GG1,GG2,G_REF,dsg_modi,dsg_mode

Examples

result dataframe

      loci    T_gt_GT  TG1    TG2      T_REF         G_gt_GT       GG1           GG2           G_REF            dsg_modi   dsg_mode
 1__10034928     1/1   gatg   gatg gatggatggatggatg     0/0 gatggatggatggatg gatggatggatggatg gatggatggatggatg       24 mutate_all
 1__10035556     1/1  aaaac  aaaac  aaaacaaaacaaaac     0/0  aaaacaaaacaaaac  aaaacaaaacaaaac  aaaacaaaacaaaac       20 mutate_all
 1__100405174     1/1 ttgttg ttgttg  ttgttgttgttgttg     0/0  ttgttgttgttgttg  ttgttgttgttgttg  ttgttgttgttgttg       18 mutate_all

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