enable fread

jiang548 · May 1, 2022 · 62e2bd4 · 62e2bd4
1 parent 7613b16
commit 62e2bd4
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/script/cis-eQTL/common.ciseQTL.r b/script/cis-eQTL/common.ciseQTL.r
@@ -1,8 +1,9 @@
 ### common.ciseQTL.R
 ### Calculate p-values of all common cis-eQTL
 #
-y=read.table(Sys.getenv("gexp"))
-x=read.table('common.Geno.data')
+library(data.table)
+y=fread(Sys.getenv("gexp"))
+x=fread('common.Geno.data')
 y=as.matrix(y)
 x=as.matrix(x)
 y=scale(y)

diff --git a/script/cis-eQTL/low.ciseQTL.r b/script/cis-eQTL/low.ciseQTL.r
@@ -1,8 +1,8 @@
 ### low.ciseQTL.R
 ### Calculate p-values of low-freq cis-eQTL via permutation
 #
-y=read.table(Sys.getenv("gexp"))
-x=read.table('low.Geno.data')
+y=fread(Sys.getenv("gexp"))
+x=fread('low.Geno.data')
 idx=read.table('low.cispair.idx')
 y=as.matrix(y)
 x=as.matrix(x)

diff --git a/script/cis-eQTL/rare.ciseQTL.r b/script/cis-eQTL/rare.ciseQTL.r
@@ -1,8 +1,9 @@
 ### rare.ciseQTL.R
 ### Calculate p-values of rare-freq cis-eQTL via permutation
 #
-y=read.table(Sys.getenv("gexp"))
-x=read.table('rare.Geno.data')
+library(data.table)
+y=fread(Sys.getenv("gexp"))
+x=fread('rare.Geno.data')
 idx=read.table('rare.cispair.idx')
 y=as.matrix(y)
 x=as.matrix(x)