In slzhao/GTQC: GTQC: Automated Genotyping Array Quality Control and Report

knitr::opts_chunk$set(echo = TRUE)

Test

#library(here)
#source(here("R","prepare_functions.R"))
devtools::load_all(".")


#plinkBed="D:\\temp\\1kg_phase1_chrY.bed"
plinkBed="/scratch/cqs/zhaos/workSync/GTQC/20200213_pkgDev1/Affy60_BRCA_remove_duplicate_samples.chr22.bed"
dataForReport=initialize_report_parameter(plinkBed=plinkBed)

library(BSgenome.Hsapiens.UCSC.hg19)
dataForReport=preparePlinkData(plinkBed=plinkBed)
#                 select.snps=c("rs202112724","rs201588461","rs11575897","rs2534636","rs1800865"))

htmlTempl<-here("inst","template","/QcReportTemplate.Rmd")
outFile="D:\\temp\\report.html"
render(htmlTempl,output_file=outFile)

Test V2

devtools::load_all(".")

dataDir=paste0(Sys.getenv("WORKDIR"),"/GTQC/20200213_pkgDev1/")
#plinkBed=paste0(dataDir,"1kg_phase1_chrY.bed")
#dataForReport=processingPlinkData(plinkBed,
#                                  dupSnpFile=paste0(dataDir,"1kg_phase1_chrY.DupSnps"),
#                                  dupSampleFile=paste0(dataDir,"1kg_phase1_chrY.DupSamples"),
#                                  raceFile=paste0(dataDir,"1kg_phase1.race"))
plinkBed=paste0(dataDir,"1kg_phase1_chr21.bed")
dataForReport=processingPlinkData(plinkBed,
                                  dupSampleFile=paste0(dataDir,"1kg_phase1_chrY.DupSamples"),
                                  raceFile=paste0(dataDir,"1kg_phase1.race"))



library(here)
reportTemplate<-here("inst","template","/QcReportTemplate.Rmd")
#reportTemplate=system.file('templates', "QcReportTemplate.Rmd", package = 'GTQC')

outFile=paste0(plinkBed,".report.html")
render(reportTemplate,output_file=outFile)