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Commit 576b4b85 authored by Dhanaprakash Jambulingam's avatar Dhanaprakash Jambulingam
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Merge branch 'dhana' into 'master' 

Added session information file

See merge request dhajam/corplot!2
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shiny::runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
install.packages("tidyverse")
library(tidyverse)
library(MASS)
tidyverse_conflicts()
tidyverse_update()
install.packages(c("dplyr", "modelr", "stringr", "tidyr"))
library(tidyverse)
library(MASS)
tidyverse_conflicts()
tidyverse_update()
install.packages(c("dplyr", "stringr", "tidyr"))
install.packages(c("dplyr", "stringr", "tidyr"))
shiny::runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
install.packages('swirl')
library('swirl')
ls()
rm(list=ls())
install_from_swirl("R_Programming")
install_from_swirl("Data_Analysis")
swirl()
5+7
x <- 5+7
x
y <- x-3
y
z <- c(1.1,9, 3.14)
?c
z
c(z,555,z)
z*2+100
sqrt(z-1)
my_sqrt <- sqrt(z-1)
my_sqrt
my_div <- z/my_sqrt
my_div
c(1, 2, 3, 4) + c(0, 10)
c(1, 2, 3, 4) + c(0, 10, 100)
z*2+1000
my_div
shiny::runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
runApp('corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
shiny::runApp('LocusExplorer')
runApp('Dropbox/corplot/shinycorplots-master-b122d52470b8c848139a1ae7e5c932b7f82afff3')
install.packages('rsconnect')
install.packages("rsconnect")
library(IRanges)
install.packages("rsconnect")
source("https://bioconductor.org/biocLite.R")
biocLite("IRanges")
library(IRanges)
ir1 <- IRanges(start = c(1,3,5), end = c(3,5,7))
ir1
ir2 <- IRanges(start = c(1,3,5), width = 3)
ir2
all.equal(ir1, ir2)
width(ir2) <- 1
ir2
names(ir1) <- paste("A", 1:3, sep = "")
ir1
names(ir1) <- paste("A", 1:3, sep = "")
ir1
names(ir1)
dim(ir1)
?IRanges
ir3 <- IRanges(start = c(1,3,5), width = 3, names = paste('"A", 1:3, sep =""' ))
ir3
ir3 <- IRanges(start = c(1,3,5), width = 3, names = c(A1,A2,A3))
ir3 <- IRanges(start = c(1,3,5), width = 3, names = c("A1","A2","A3"))
ir3
ir3 <- IRanges(start = c(1,3,5), width = 3, names = (paste('"A", 1:3, sep =""' )))
ir3
browseVignettes("GenomicRanges")
browseVignettes("GenomicRanges")
browseVignettes("IRanges")
shiny::runApp('LocusExplorer')
shiny::runApp('tools/LocusExplorer')
shiny::runApp('LocusExplorer')
runApp('LocusExplorer')
install.packages("LDheatmap")
library("LDheatmap")
library(LDheatmap)
install.packages("snpStats")
source("https://bioconductor.org/biocLite.R")
biocLite("snpStats")
library("LDheatmap")
install.packages("LDheatmap")
library("LDheatmap")
data("CEUData")
data
MyHeatmap <- LDheatmap(CEUSNP, CEUDist, LDmeasure="r", title="Pairwise LD in r^2", add.map=TRUE, SNP.name=c("rs2283092", "rs6979287"), color=grey.colors(20), name="myLDgrob", add.key=TRUE)
MyHeatmap
plot(MyHeatmap)
xy<-data("CEUData")
xy
View("CEUData")
shiny::runApp('LocusExplorer')
library(QCGWAS)
install.packages("QCGWAS")
c
shiny::runApp('LocusExplorer')
runApp('LocusExplorer')
mat = matrix(sample(100, 25), 5)
mat
sample(100,25)
sample(1000,25)
sample(10,25)
sample(10,9)
sample(10,10)
sample(10,11)
mat = matrix(sample(100, 25), 6)
mat = matrix(sample(100, 36), 6)
mat
library(readr)
locus <- read_delim("~/tools/rasp/locus.tsv",
"\t", escape_double = FALSE, trim_ws = TRUE)
View(locus)
library(gap)
options(stringsAsFactors=FALSE)
p <- with(locus,data.frame(SNP=NAME,PVAL))
p
hit <- subset(p,PVAL==min(PVAL,na.rm=TRUE))$SNP
hit
install.packages("NCBI2R")
install.packages("~/Downloads/NCBI2R_1.4.7.tar.gz", repos = NULL, type = "source")
library(NCBI2R)
# LD under build 36
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapmap)
library(IRanges)
library(gap)
library(NCBI2R)
GetSNPPosHapMap()
GetSNPPosHapMap("rs2074187")
options(stringsAsFactors=FALSE)
p <- with(locus,data.frame(SNP=NAME,PVAL))
p
hit <- subset(p,PVAL==min(PVAL,na.rm=TRUE))$SNP
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapmap)
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapMap)
hit <- subset(p,PVAL==min(PVAL,na.rm=TRUE))$SNP
hit
p$SNP
pos <- apply(as.data.frame(p$SNP),2,GetSNPPosHapMap)
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapMap)
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapmap)
library(IRanges)
library(S4Vectors)
library(gap)
library(NCBI2R)
options(stringsAsFactors=FALSE)
p <- with(locus,data.frame(SNP=NAME,PVAL))
hit <- subset(p,PVAL==min(PVAL,na.rm=TRUE))$SNP
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapmap)
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapMap)
remove.packages("NCBI2R", lib="~/R/x86_64-pc-linux-gnu-library/3.4")
install.packages("~/Downloads/NCBI2R-1.4.6.tar.gz", repos = NULL, type = "source")
library(NCBI2R)
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapMap)
library(NCBI2R)
GetSNPPosHapMap("rs2074187")
GetSNPInfo("rs2074187")
library(readr)
snplist <- read_csv("~/Downloads/snplist.csv",
col_names = FALSE)
View(snplist)
GetSNPInfo(snplist)
snp1<-as.data.frame(snplist)
snp1
GetSNPInfo(snp1)
View(locus)
options(stringsAsFactors=FALSE)
p <- with(locus,data.frame(SNP=NAME,PVAL))
p
hit <- subset(p,PVAL==min(PVAL,na.rm=TRUE))$SNP
require(gap.datasets)
install.packages("gap.datasets")
require(gap.datasets)
library(NCBI2R)
chr_pos <- GetSNPInfo(with(p,SNP))[c("chr","chrpos")]
View(chr_pos)
l <- with(chr_pos,min(as.numeric(chrpos),na.rm=TRUE))
u <- with(chr_pos,max(as.numeric(chrpos),na.rm=TRUE))
LD <- with(chr_pos,GetLDInfo(unique(chr),l,u))
l <- with(chr_pos,min(as.numeric(chrpos),na.rm=TRUE))
l
u <- with(chr_pos,max(as.numeric(chrpos),na.rm=TRUE))
u
LD <- with(chr_pos,GetLDInfo(unique(chr),l,u))
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapmap)
pos <- apply(as.data.frame(p$SNP),1,GetSNPPosHapMap)
LD <- with(chr_pos,9,l,u))
LD <- with(chr_pos,9,l,u)
LD
LD <- with(chr_pos,9,21890327,22385640)
LD
hit_LD <- subset(LD,SNPA==hit)
hit
hit_LD <- subset(LD,rs10811661)
LD <- with(chr_pos,unique(9),l,u)
LD
hit_LD <- subset(LD,SNPA==hit)
info <- GetSNPInfo(p$SNP)
info
info <- GetSNPInfo(p$SNP)
haldane <- function(x) 0.5*(1-exp(-2*x))
locus <- with(info, data.frame(CHR=chr,POS=chrpos,NAME=marker,
DIST=(chrpos-min(chrpos))/1000000,
THETA=haldane((chrpos-min(chrpos))/100000000)))
locus
locus1 <- with(info, data.frame(CHR=chr,POS=chrpos,NAME=marker,
DIST=(chrpos-min(chrpos))/1000000,
THETA=haldane((chrpos-min(chrpos))/100000000)))
locus1
locus <- with(info, data.frame(CHR=chr,POS=chrpos,NAME=marker,
DIST=(chrpos-min(chrpos))/1000000,
THETA=haldane((chrpos-min(chrpos))/100000000)))
locus <- merge.data.frame(locus,hit_LD,by.x="NAME",by.y="SNPB",all=TRUE)
locus <- merge.data.frame(locus,p,by.x="NAME",by.y="SNP",all=TRUE)
locus
locus <- subset(locus,!is.na(POS))
ann <- AnnotateSNPList(p$SNP)
shiny::runApp('LocusExplorer')
shiny::runApp('Downloads/correlation_plot-v2dev')
.project deleted 100755 → 0
View file @ 325325f0
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>corplots</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>de.walware.statet.r.builders.RSupport</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>de.walware.statet.base.StatetNature</nature>
<nature>de.walware.statet.r.RNature</nature>
</natures>
</projectDescription>
Markdown/RSessionInfo.Rmd
View file @ 576b4b85
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.5.2 (2018-12-20)
os Ubuntu 18.04.1 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Helsinki
date 2019-01-08
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 3.5.1)
annotate 1.58.0 2018-11-14 [1] Bioconductor
AnnotationDbi * 1.42.1 2018-11-14 [1] Bioconductor
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.1)
backports 1.1.2 2017-12-13 [1] CRAN (R 3.5.1)
base64enc 0.1-4 2018-11-14 [1] local
bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.1)
bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.1)
Biobase * 2.40.0 2018-11-14 [1] Bioconductor
BiocGenerics * 0.26.0 2018-11-14 [1] Bioconductor
biomaRt * 2.36.1 2018-11-14 [1] Bioconductor
bit 1.1-14 2018-05-29 [1] CRAN (R 3.5.1)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.5.1)
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.5.1)
blob 1.1.1 2018-03-25 [1] CRAN (R 3.5.1)
checkmate 1.8.5 2017-10-24 [1] CRAN (R 3.5.1)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.1)
clipr * 0.4.1 2018-06-23 [1] CRAN (R 3.5.2)
cluster * 2.0.7-1 2018-04-09 [1] CRAN (R 3.5.1)
codetools 0.2-16 2018-12-24 [4] CRAN (R 3.5.2)
colorspace 1.4-0 2018-11-05 [1] R-Forge (R 3.5.1)
coreheat * 0.1-5 2018-11-14 [2] local
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1)
data.table * 1.11.8 2018-09-30 [1] CRAN (R 3.5.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.5.1)
DEoptimR 1.0-8 2016-11-19 [1] CRAN (R 3.5.1)
digest * 0.6.18 2018-10-10 [1] CRAN (R 3.5.1)
doParallel 1.0.14 2018-09-21 [2] R-Forge (R 3.5.1)
dplyr 0.7.8 2018-11-10 [1] CRAN (R 3.5.1)
DT * 0.5 2018-11-05 [2] CRAN (R 3.5.1)
dynamicTreeCut 1.63-1 2016-03-11 [2] CRAN (R 3.5.1)
evaluate 0.12 2018-10-09 [1] CRAN (R 3.5.1)
fastcluster 1.1.25 2018-06-07 [1] CRAN (R 3.5.1)
fit.models 0.5-14 2017-04-06 [2] CRAN (R 3.5.1)
foreach * 1.5.1 2018-08-27 [1] R-Forge (R 3.5.1)
foreign 0.8-71 2018-07-20 [4] CRAN (R 3.5.1)
Formula 1.2-3 2018-05-03 [1] CRAN (R 3.5.1)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.5.1)
genefilter * 1.62.0 2018-11-14 [1] Bioconductor
ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.5.1)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.1)
GO.db 3.6.0 2018-11-14 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.5.1)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.1)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.5.1)
heatmapGen * 0.1-0 2018-11-14 [2] local
heatmapGen2 * 0.1-3 2018-11-14 [2] local
Heatplus * 2.26.0 2018-11-14 [1] Bioconductor
Hmisc 4.1-1 2018-01-03 [1] CRAN (R 3.5.1)
hms 0.4.2 2018-03-10 [1] CRAN (R 3.5.1)
htmlTable 1.12 2018-05-26 [1] CRAN (R 3.5.1)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.1)
htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.5.1)
httpuv 1.4.5 2018-07-19 [1] CRAN (R 3.5.1)
httr 1.3.1 2017-08-20 [1] CRAN (R 3.5.1)
impute 1.54.0 2018-11-14 [2] Bioconductor
IRanges * 2.14.12 2018-09-20 [1] Bioconductor
iterators 1.0.11 2018-07-05 [1] R-Forge (R 3.5.1)
jsonlite 1.5 2017-06-01 [1] CRAN (R 3.5.1)
knitr * 1.20 2018-02-20 [1] CRAN (R 3.5.1)
later 0.7.5 2018-09-18 [1] CRAN (R 3.5.1)
lattice 0.20-38 2018-11-04 [4] CRAN (R 3.5.1)
latticeExtra 0.6-28 2016-02-09 [1] CRAN (R 3.5.1)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.1)
markdown 0.8.1 2018-11-14 [1] local
MASS 7.3-51.1 2018-11-01 [4] CRAN (R 3.5.1)
Matrix 1.2-15 2018-11-01 [4] CRAN (R 3.5.1)
matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.5.1)
medseqr * 0.4-10 2018-11-14 [2] local
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.1)
mime 0.6.1 2018-11-14 [1] local
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.1)
mvtnorm 1.0-8 2018-05-31 [1] CRAN (R 3.5.1)
nnet 7.3-12 2016-02-02 [4] CRAN (R 3.5.0)
org.Hs.eg.db * 3.6.0 2018-11-14 [1] Bioconductor
org.Mm.eg.db * 3.6.0 2018-11-14 [1] Bioconductor
PAMhm * 0.1-1 2018-11-14 [2] local
pander * 0.6.3 2018-11-06 [1] CRAN (R 3.5.2)
pcaPP 1.9-73 2018-01-14 [1] CRAN (R 3.5.1)
pillar 1.3.0 2018-07-14 [1] CRAN (R 3.5.1)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.1)
plyr * 1.8.4 2016-06-08 [1] CRAN (R 3.5.1)
preprocessCore 1.42.0 2018-11-14 [1] Bioconductor
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.1)
progress 1.2.0 2018-06-14 [1] CRAN (R 3.5.1)
promises 1.0.1 2018-04-13 [1] CRAN (R 3.5.1)
purrr 0.2.5 2018-05-29 [1] CRAN (R 3.5.1)
R.methodsS3 * 1.7.1 2016-02-16 [1] CRAN (R 3.5.1)
R.oo * 1.22.0 2018-04-22 [1] CRAN (R 3.5.1)
R.utils * 2.7.0 2018-08-27 [1] CRAN (R 3.5.1)
R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.1)
RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 3.5.1)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.1)
RCurl 1.96-0 2018-11-14 [1] local
readR * 0.2-1 2018-11-14 [2] local
rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.5.1)
rmarkdown * 1.10 2018-06-11 [1] CRAN (R 3.5.1)
robust 0.4-18 2017-04-27 [2] R-Forge (R 3.5.1)
robustbase 0.93-3 2018-09-21 [1] CRAN (R 3.5.1)
rpart 4.1-13 2018-02-23 [4] CRAN (R 3.5.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.1)
rrcov 1.4-7 2018-11-15 [1] CRAN (R 3.5.1)
RSQLite 2.1.1 2018-05-06 [1] CRAN (R 3.5.1)
rstudioapi 0.8 2018-10-02 [1] CRAN (R 3.5.1)
S4Vectors * 0.18.3 2018-11-14 [1] Bioconductor
scales * 1.0.0 2018-08-09 [1] CRAN (R 3.5.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.1)
shiny * 1.2.0 2018-11-02 [1] CRAN (R 3.5.1)
shinyBS * 0.61 2015-03-31 [1] CRAN (R 3.5.1)
shinyjs 1.0 2018-01-08 [1] CRAN (R 3.5.1)
shinythemes * 1.1.2 2018-11-06 [1] CRAN (R 3.5.1)
stringi 1.2.4 2018-07-20 [1] CRAN (R 3.5.1)
stringr 1.3.1 2018-05-10 [1] CRAN (R 3.5.1)
survival 2.43-3 2018-11-26 [4] CRAN (R 3.5.1)
tibble 1.4.2 2018-01-22 [1] CRAN (R 3.5.1)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.1)
WGCNA 1.66 2018-10-24 [2] CRAN (R 3.5.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.1)
XML 3.99-0 2018-11-14 [1] local
xtable 1.8-3 2018-08-29 [1] CRAN (R 3.5.1)
yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.1)
[1] /home/djambulingam/R/x86_64-pc-linux-gnu-library/3.5
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
server.R
View file @ 576b4b85
......@@ -613,10 +613,9 @@ shinyServer(function(input, output, session) {
showModal(
modalDialog(
HTML(
'<img src="http://www.google.nl/images/branding/googlelogo/2x/googlelogo_color_272x92dp.png">'
'<img src="https://gitlab.utu.fi/dhajam/corplot/blob/master/Markdown/FAQ.md">'
),
title = "Example expression file",
"This is a somewhat important message, listen carefully human.",
easyClose = TRUE,
footer = NULL
)
......
Supports Markdown
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