Merge branch 'doc'

choishingwan · Jul 30, 2019 · a850a69 · a850a69
2 parents 68fe907 + 9a2b2f9
commit a850a69
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Showing 5 changed files with 17 additions and 7 deletions.
diff --git a/Makefile b/Makefile
@@ -7,7 +7,7 @@ SERVER := -L /usr/lib/x86_64-redhat-linux5E/lib64
 GCC := -Wl,--no-whole-archive  -static-libstdc++ -static-libgcc -static
 CSRC := src/*.c
 CPPSRC := src/*.cpp
-OBJ := gzstream.o bgen_lib.o binaryplink.o genotype.o misc.o prslice.o regression.o snp.o binarygen.o commander.o main.o plink_common.o prsice.o region.o reporter.o
+OBJ := gzstream.o bgen_lib.o binaryplink.o genotype.o misc.o dcdflib.o regression.o snp.o binarygen.o commander.o main.o plink_common.o prsice.o region.o reporter.o
 
 %.o: src/%.c
 		$(CXX) $(CXXFLAGS) $(INCLUDES) -c $< -o $@

diff --git a/PRSice.R b/PRSice.R
@@ -19,7 +19,7 @@ In_Regression <-
     R2 <-
     print.p <- R <- P <- value <- Phenotype <- Set <- PRS.R2 <- LCI <- UCI <- quant.ref <- NULL
 
-r.version <- "2.2.4"
+r.version <- "2.2.5"
 # Help Messages --------------------------------------
 help_message <-
 "usage: Rscript PRSice.R [options] <-b base_file> <-t target_file> <--prsice prsice_location>\n
@@ -322,6 +322,8 @@ help_message <-
                             seed and same input is provided, same result\n
                             can be generated\n
     --thread        | -n    Number of thread use\n
+    --use-ref-maf           When specified, missingness imputation will be\n
+                            performed based on the reference samples\n
     --x-range               Range of SNPs to be excluded from the whole\n
                             analysis. It can either be a single bed file\n
                             or a comma seperated list of range. Range must\n
@@ -542,6 +544,7 @@ option_list <- list(
   make_option(c("--non-cumulate"), action = "store_true", dest = "non_cumulate"),
   make_option(c("--pearson"), action = "store_true"),
   make_option(c("-n", "--thread"), type = "numeric"),
+  make_option(c("--use-ref-maf"), action = "store_true", dest = "use_ref_maf"),
   make_option(c("--x-range"), type = "character", dest="x_range"),
   #R Specified options
   make_option(c("--plot"), action = "store_true"),
@@ -691,7 +694,8 @@ flags <-
         "no-y",
         "non-cumulate",
         "or",
-        "print-snp"
+        "print-snp",
+        "use-ref-maf"
     )
 # Skip PRSice core function if only plotting is requirec
 if (!provided("plot", argv)) {

diff --git a/docs/index.md b/docs/index.md
@@ -15,10 +15,10 @@ PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating
 # Executable downloads
 | Operating System | Link |
 | -----------------|:----:|
-| Linux 64-bit | [v2.2.3](https://github.com/choishingwan/PRSice/releases/download/2.2.3/PRSice_linux.zip) |
-| OS X 64-bit | [v2.2.3](https://github.com/choishingwan/PRSice/releases/download/2.2.3/PRSice_mac.zip) |
-| Windows 32-bit | [v2.2.3](https://github.com/choishingwan/PRSice/releases/download/2.2.3/PRSice_win32.zip) |
-| Windows 64-bit | [v2.2.3](https://github.com/choishingwan/PRSice/releases/download/2.2.3/PRSice_win64.zip) |
+| Linux 64-bit | [v2.2.5](https://github.com/choishingwan/PRSice/releases/download/2.2.5/PRSice_linux.zip) |
+| OS X 64-bit | [v2.2.5](https://github.com/choishingwan/PRSice/releases/download/2.2.5/PRSice_mac.zip) |
+| Windows 32-bit | [v2.2.5](https://github.com/choishingwan/PRSice/releases/download/2.2.5/PRSice_win32.zip) |
+| Windows 64-bit | [v2.2.5](https://github.com/choishingwan/PRSice/releases/download/2.2.5/PRSice_win64.zip) |
 
 !!! Caution 
 

diff --git a/help_messages.txt b/help_messages.txt
@@ -280,6 +280,8 @@ m_help_message =
        "                            seed and same input is provided, same result\n"
        "                            can be generated\n"
        "    --thread        | -n    Number of thread use\n"
+       "    --use-ref-maf           When specified, missingness imputation will be\n"
+       "                            performed based on the reference samples\n"
        "    --x-range               Range of SNPs to be excluded from the whole\n"
        "                            analysis. It can either be a single bed file\n"
        "                            or a comma seperated list of range. Range must\n"

diff --git a/src/commander.cpp b/src/commander.cpp
@@ -1024,6 +1024,10 @@ void Commander::set_help_message()
           "result\n"
           "                            can be generated\n"
           "    --thread        | -n    Number of thread use\n"
+          "    --use-ref-maf           When specified, missingness imputation "
+          "will be\n"
+          "                            performed based on the reference "
+          "samples\n"
           "    --x-range               Range of SNPs to be excluded from the "
           "whole\n"
           "                            analysis. It can either be a single bed "