## ----- global_options，包括= false ------------------------------------------------------------------------------------------------------------------------------------------ knitr :: opts_chunk $ set（警告= false，message = false）## ---- load_package ------------------------------------------------------------------------------------------------------------------------------------------- library(scoreInvHap) ## ---- eval=FALSE--------------------------------------------------------------------------------------------------＃library（snpstats）＃＃##从床上＃snps < - read.plink（“ example.bed”）＃＃##从pedfile＃snps < - 阅读。-------------------------------------库（variantannotation）vcf_file <-System.file（“ extdata”，“ example.vcf”，package = =“ ScoreInvhap”）VCF <-ReadVCF（VCF_FILE，“ HG19”）VCF ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------]VCF）检查VCF < - 检查$ GENOS ## ----分类--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- res <-ScoreInvhap（snplist = vcf，inv =“ inv7_005”）res ## -- classify_par，eval = false ----------------------------------------------------------------------------------------＃res <-Scoreinvhap（snplist = vcf，inv=“ Inv7_005”，＃bpparam = Biocparallelal :: MulticoreParam（8））## ----------------------------------------------------------------------------------------------------------------------＃获取分类头（分类（RES））＃获得分数头（分数（RES））## ---- ScoreInvhap分数-------------------------------------------------------------------------------------------------------------------＃获得最大得分头（MaxScores（RES））＃获取差异得分头（DIFFSCORES（RES））## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- plotScores(res, pch = 16, main = "QC based on scores") ## ----------------------------------------------------------------------------- # Get Number of scores used head(numSNPs(res)) # Get call rate head(propSNPs(res)) ## ----------------------------------------------------------------------------- plotCallRate(res, main = "Call Rate QC") ## ----------------------------------------------------------------------------- ## No filtering length(classification(res)) ## QC filtering length(classification(res, minDiff = 0.1, callRate = 0.9)) ## ----------------------------------------------------------------------------- ## Inversion classification table(classification(res)) ## Haplotype classification table(classification(res, inversion = FALSE)) ## ---- classify imputed-------------------------------------------------------- res_imp <- scoreInvHap(SNPlist = vcf, inv = "inv7_005", probs = TRUE) res_imp ## ---- compare classifications------------------------------------------------- table(PostProbs = classification(res_imp), BestGuess = classification(res)) ## ----------------------------------------------------------------------------- data(inversionGR) inversionGR ## ----------------------------------------------------------------------------- sessionInfo()