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add option that allows running clump locally (after supplying bed files and plink path) #9

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add option that allows running clump locally (after supplying bed files and plink path) #9

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4 changes: 2 additions & 2 deletions R/calculate_SP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
#'
#' @examples
calculate_SP <- function(input.df,trait.names,run_ldsc=TRUE,run_MR=TRUE,saveRFiles=TRUE,hm3=NA,ld=NA,nStep=2,
SP_single=3,SP_pair=50,SNP_filter=10,SNP_filter_ldsc=NA,nCores=1,M=1e7){
SP_single=3,SP_pair=50,SNP_filter=10,SNP_filter_ldsc=NA,nCores=1,M=1e7, b_file=NULL, plink_path=NULL){

if(nStep>2 || nStep<1){
cat(print("Please choose 1 or 2 for the number of analysis steps\n"))
Expand All @@ -54,7 +54,7 @@ calculate_SP <- function(input.df,trait.names,run_ldsc=TRUE,run_MR=TRUE,saveRFil
OUT = trait.names[2]

# Get estimates of starting points from LDSC and standard MR method (IVW)
SP = gettingSP_ldscMR(input.df,trait.names,run_ldsc,run_MR,saveRFiles,SNP_filter_ldsc,hm3,ld)
SP = gettingSP_ldscMR(input.df,trait.names,run_ldsc,run_MR,saveRFiles,SNP_filter_ldsc,hm3,ld, b_file = b_file, plink_path = plink_path)
i_XY = as.numeric(SP[[1]])
axy_MR = as.numeric(SP[[2]])
ayx_MR = as.numeric(SP[[3]])
Expand Down
52 changes: 49 additions & 3 deletions R/gettingSP_ldscMR.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,44 @@
#' @return
#' @keywords internal
# NOT EXPORTED @export
gettingSP_ldscMR = function(input.df,trait.names,run_ldsc=TRUE,run_MR=TRUE,saveRFiles=TRUE,SNP_filter_ldsc,hm3,ld){
ld_clump_local <- function(dat, clump_kb = 10000, clump_r2 = 0.001, clump_p1 = 1, clump_p2 = 1, pop = "EUR", b_file, plink_path) {
pval_column <- "pval.exposure"
if (!is.data.frame(dat)) {
stop("Expecting data frame returned from format_data")
}
if ("pval.exposure" %in% names(dat) & "pval.outcome" %in%
names(dat)) {
message("pval.exposure and pval.outcome columns present. Using pval.exposure for clumping.")
} else if (!"pval.exposure" %in% names(dat) & "pval.outcome" %in%
names(dat)) {
message("pval.exposure column not present, using pval.outcome column for clumping.")
pval_column <- "pval.outcome"
} else if (!"pval.exposure" %in% names(dat)) {
message("pval.exposure not present, setting clumping p-value to 0.99 for all variants")
dat$pval.exposure <- 0.99
} else {
pval_column <- "pval.exposure"
}
if (!"id.exposure" %in% names(dat)) {
dat$id.exposure <- random_string(1)
}
d <- data.frame(
rsid = dat$SNP, pval = dat[[pval_column]],
id = dat$id.exposure
)
out <- ieugwasr::ld_clump(d,
clump_kb = clump_kb, clump_r2 = clump_r2,
clump_p = clump_p1, pop = pop,
bfile = b_file, plink_bin = plink_path
)
keep <- paste(dat$SNP, dat$id.exposure) %in% paste(
out$rsid,
out$id
)
return(dat[keep, ])
}

gettingSP_ldscMR = function(input.df,trait.names,run_ldsc=TRUE,run_MR=TRUE,saveRFiles=TRUE,SNP_filter_ldsc,hm3,ld,plink_path=NULL,b_file=NULL){

EXP = trait.names[1]
OUT = trait.names[2]
Expand Down Expand Up @@ -146,7 +183,12 @@ gettingSP_ldscMR = function(input.df,trait.names,run_ldsc=TRUE,run_MR=TRUE,saveR
exp_data = c()
for (x in 1:length(clump_bin)) {
temp = exp_dat[exp_dat$SNP %in% clump_bin[[x]]$SNP,]
temp1 = TwoSampleMR::clump_data(temp)
if (is.null(plink_path)) {
temp1 = TwoSampleMR::clump_data(temp)
} else {
temp1 = ld_clump_local(temp, plink_path=plink_path,b_file = b_file)

}
exp_data=rbind(exp_data,temp1)
}

Expand Down Expand Up @@ -237,7 +279,11 @@ gettingSP_ldscMR = function(input.df,trait.names,run_ldsc=TRUE,run_MR=TRUE,saveR
exp_data = c()
for (x in 1:length(clump_bin)) {
temp = exp_dat[exp_dat$SNP %in% clump_bin[[x]]$SNP,]
temp1 = TwoSampleMR::clump_data(temp)
if (is.null(plink_path)) {
temp1 = TwoSampleMR::clump_data(temp)
} else {
temp1 = ld_clump_local(temp, plink_path=plink_path,b_file = b_file)
}
exp_data=rbind(exp_data,temp1)
}

Expand Down