Nothing
## ----eval=FALSE----------------------------------------------------------
# library("bmass");
# HDL <- read.table("jointGwasMc_HDL.formatted.QCed.txt.gz", header=T);
# LDL <- read.table("jointGwasMc_LDL.formatted.QCed.HDLMatch.txt.gz", header=T);
# TG <- read.table("jointGwasMc_TG.formatted.QCed.HDLMatch.txt.gz", header=T);
# TC <- read.table("jointGwasMc_TC.formatted.QCed.HDLMatch.txt.gz", header=T);
# load("bmassDirectory/data/GlobalLipids2013.GWASsnps.rda");
# Phenotypes <- c("HDL", "LDL", "TG", "TC");
# bmassResults <- bmass(Phenotypes, GlobalLipids2013.GWASsnps);
## ----eval=FALSE----------------------------------------------------------
# > summary(bmassResults)
# Length Class Mode
# MarginalSNPs 3 -none- list
# PreviousSNPs 4 -none- list
# NewSNPs 3 -none- list
# LogFile 20 -none- character
# ZScoresCorMatrix 16 -none- numeric
# Models 324 -none- numeric
# ModelPriors 1134 -none- numeric
# GWASlogBFMinThreshold 1 -none- numeric
## ----eval=FALSE----------------------------------------------------------
# > summary(bmassResults$NewSNPs)
# Length Class Mode
# SNPs 30 data.frame list
# logBFs 5427 -none- numeric
# Posteriors 5427 -none- numeric
## ----eval=FALSE----------------------------------------------------------
# > head(bmassResults$NewSNPs$SNPs, n=3)
# ChrBP Chr BP Marker MAF A1 HDL_A2 HDL_Direction
# 1704 10_101902054 10 101902054 rs2862954 0.4631 C T +
# 72106 10_5839619 10 5839619 rs2275774 0.1781 G A +
# 118903 11_109521729 11 109521729 rs661171 0.2876 T G +
# HDL_pValue HDL_N HDL_ZScore LDL_Direction LDL_pValue LDL_N
# 1704 1.287e-06 186893 4.841751 + 5.875e-01 172821.0
# 72106 7.601e-07 179144 4.945343 - 7.773e-05 165198.0
# 118903 1.705e-06 186946 4.785573 + 1.653e-02 172877.9
# LDL_ZScore TG_Direction TG_pValue TG_N TG_ZScore TC_Direction
# 1704 0.5424624 + 0.013930 177587.1 2.459063 +
# 72106 -3.9512933 - 0.001035 169853.0 -3.280836 -
# 118903 2.3969983 - 0.155800 177645.0 -1.419340 +
# TC_pValue TC_N TC_ZScore GWASannot mvstat mvstat_log10pVal unistat
# 1704 2.526e-04 187083 3.659609 0 48.70946 9.173067 23.44255
# 72106 1.911e-02 179333 -2.343378 0 38.26288 7.004804 24.45642
# 118903 1.785e-05 187131 4.290215 0 37.84098 6.917765 22.90171
# unistat_log10pVal Nmin logBFWeightedAvg
# 1704 5.890421 172821.0 7.068306
# 72106 6.119129 165198.0 5.447201
# 118903 5.768276 172877.9 5.438490
## ----eval=FALSE----------------------------------------------------------
# > dim(bmassResults$NewSNPs$logBFs)
# [1] 81 67
# > bmassResults$NewSNPs$logBFs[1:5,1:10]
# HDL LDL TG TC 10_101902054 10_5839619 11_109521729 11_13313759
# [1,] 0 0 0 0 0.000000 0.0000000 0.0000000 0.00000000
# [2,] 1 0 0 0 -233.831047 -235.0781367 -234.6670299 -234.15472067
# [3,] 2 0 0 0 0.000000 0.0000000 0.0000000 0.00000000
# [4,] 0 1 0 0 0.165855 0.3172489 -0.1100418 0.06393596
# [5,] 1 1 0 0 -64.774919 -66.2959645 -69.2388829 -69.93309528
# 11_45696596 11_47251202
# [1,] 0.00000000 0.00000000
# [2,] -231.68478695 -219.10321932
# [3,] 0.00000000 0.00000000
# [4,] -0.04838241 0.04997886
# [5,] -65.59917325 -45.04269241
## ----eval=FALSE----------------------------------------------------------
# > summary(bmassResults$PreviousSNPs)
# Length Class Mode
# logBFs 12069 -none- numeric
# SNPs 30 data.frame list
# DontPassSNPs 30 data.frame list
# Posteriors 12069 -none- numeric
## ----eval=FALSE----------------------------------------------------------
# > summary(bmassResults$MarginalSNPs)
# Length Class Mode
# SNPs 30 data.frame list
# logBFs 20493 -none- numeric
# Posteriors 20493 -none- numeric
## ----eval=FALSE----------------------------------------------------------
# > bmassResults$ZScoresCorMatrix
# HDL_ZScore LDL_ZScore TG_ZScore TC_ZScore
# HDL_ZScore 1.0000000 -0.0872789 -0.3655508 0.1523894
# LDL_ZScore -0.0872789 1.0000000 0.1607208 0.8223175
# TG_ZScore -0.3655508 0.1607208 1.0000000 0.2892982
# TC_ZScore 0.1523894 0.8223175 0.2892982 1.0000000
## ----eval=FALSE----------------------------------------------------------
# > dim(bmassResults$Models)
# [1] 81 4
# > head(bmassResults$Models)
# HDL LDL TG TC
# [1,] 0 0 0 0
# [2,] 1 0 0 0
# [3,] 2 0 0 0
# [4,] 0 1 0 0
# [5,] 1 1 0 0
# [6,] 2 1 0 0
## ----eval=FALSE----------------------------------------------------------
# > length(bmassResults$ModelPriors)
# [1] 1134
# > bmassResults[c("ModelPriorMatrix", "LogFile")] <- GetModelPriorMatrix(Phenotypes, bmassResults$Models, bmassResults$ModelPriors, bmassResults$LogFile)
# > head(bmassResults$ModelPriorMatrix)
# HDL LDL TG TC Prior Cumm_Prior OrigOrder
# 1 1 2 1 1 0.32744537 0.3274454 44
# 2 1 2 2 1 0.13788501 0.4653304 53
# 3 1 1 1 2 0.11727440 0.5826048 68
# 4 1 1 1 1 0.07801825 0.6606230 41
# 5 1 2 1 2 0.06210658 0.7227296 71
# 6 2 1 2 2 0.05698876 0.7797184 78
## ----eval=FALSE----------------------------------------------------------
# > bmassResults$GWASlogBFMinThreshold
# [1] 4.289906
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