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Add parameter to XPASS function to allow for locally saved LD blocks in different builds #5

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Add parameter to XPASS function to allow for locally saved LD blocks in different builds #5

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880c10d
hg38
May 12, 2021
466dde5
Merge branch 'master' of github.com:bbitarello/XPASS
May 12, 2021
6b7a96e
Merge branch 'YangLabHKUST:master' into master
May 17, 2021
6fee041
Merge branch 'YangLabHKUST:master' into master
May 18, 2021
25dd6cf
add option for hg38
May 18, 2021
e7876b0
Merge branch 'master' of github.com:bbitarello/XPASS
May 18, 2021
495b8bf
ld blocks for hg38
May 18, 2021
bf9438e
add line for hg38 alternative
May 18, 2021
182f4ef
readme
May 18, 2021
e2eb95e
fourier
May 18, 2021
2af8e00
fourier oops
May 18, 2021
5584f97
fourier oops2
May 18, 2021
a8357bd
fix ifelse statement
May 19, 2021
6eaf67c
rm index
May 19, 2021
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12 changes: 7 additions & 5 deletions R/XPASS.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,9 +38,9 @@
#' See vignette.
#' @export

XPASS <- function(file_z1,file_z2,file_ref1,file_ref2=NULL,file_cov1=NULL,file_cov2=NULL,file_predGeno=NULL,K1=NULL,K2=NULL,K12=NULL,X1=NULL,X2=NULL,
snps_fe1=NULL,snps_fe2=NULL,snp_list=NULL,
sd_method="Chromosome",pop="EUR",compPosMean=T,use_CG=T,compPRS=F,file_out=""){
XPASS <- function(file_z1,file_z2,file_ref1,file_ref2=NULL,file_cov1=NULL,
file_cov2=NULL,file_predGeno=NULL,K1=NULL,K2=NULL,K12=NULL,X1=NULL,X2=NULL,snps_fe1=NULL,snps_fe2=NULL,
snp_list=NULL,sd_method="Chromosome",pop="EUR",compPosMean=T, use_CG=T,compPRS=T,file_out="", dir="XPASS/inst/extdata/"){
if(nchar(file_out)>0){
cat("Writing to log file: ",file_out,".log\n",sep="")
sink(paste0(file_out,".log"),append=F,split=T)
Expand Down Expand Up @@ -76,7 +76,7 @@ XPASS <- function(file_z1,file_z2,file_ref1,file_ref2=NULL,file_cov1=NULL,file_c
test_info <- fread(paste(file_predGeno,".bim",sep=""),data.table = F,stringsAsFactors = F)
colnames(test_info) <- c("CHR","SNP","POS","BP","A1","A2")
cat(nrow(test_info)," SNPs found in test file.\n",sep = "")

snps <- intersect(test_info$SNP,snps)
}

Expand Down Expand Up @@ -301,7 +301,7 @@ XPASS <- function(file_z1,file_z2,file_ref1,file_ref2=NULL,file_cov1=NULL,file_c

if(sd_method=="LD_block"|compPosMean){
cat("Assigning SNPs to LD Blocks...\n")
block <- read.table(system.file("extdata", paste0(pop,"_fourier_ls-all.bed"), package = "XPASS"),header = T)
block <- read.table(file=ifelse(dir==NULL, system.file("extdata", paste0(pop,"_fourier_ls-all.bed"), package = "XPASS"),paste0(dir,pop, "_fourier_ls-all.bed")), header=T)
group <- rep(0,nrow(zf1))
idx_group <- 1
for(i in 1:22){
Expand Down Expand Up @@ -419,13 +419,15 @@ XPASS <- function(file_z1,file_z2,file_ref1,file_ref2=NULL,file_cov1=NULL,file_c
fam_test <- fread(paste0(file_predGeno,".fam"))
test_geno <- read_data(file_predGeno,fillMiss = "zero")
Xtest <- test_geno$X[,idx_test]
print(head(Xtest)) #debug

# remove SNPs shhowing no variation in the training genotypes
Xtest <- Xtest[,!no_var]
test_info <- test_info[!no_var,]

# align alleles in test genotype based on the first ref
ind_ref <- ref1_info$A1!=test_info$A1
traceback() #debug
if(sum(ind_ref)>0){
Xtest[,ind_ref] <- 1-(Xtest[,ind_ref]-1)
cat(sum(ind_ref)," SNPs in the test genotypes are alligned for alleles according to the first.\n",sep="")
Expand Down
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