diff --git a/.RData b/.RData deleted file mode 100755 index 96a0f8c3dee906aa7f088292cdbb0a0b49894660..0000000000000000000000000000000000000000 Binary files a/.RData and /dev/null differ diff --git a/.Rhistory b/.Rhistory deleted file mode 100755 index 0f403aa9f162f6c9605a57e99cb60f6cb7defa19..0000000000000000000000000000000000000000 --- a/.Rhistory +++ /dev/null @@ -1,232 +0,0 @@ -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') diff --git a/.project b/.project deleted file mode 100755 index 75287b0293e92c7a292ba827671135ef56db2518..0000000000000000000000000000000000000000 --- a/.project +++ /dev/null @@ -1,18 +0,0 @@ -<?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> diff --git a/Markdown/RSessionInfo.Rmd b/Markdown/RSessionInfo.Rmd index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..21a3418e82cea626ac3022d258dcb02a530129f2 100755 --- a/Markdown/RSessionInfo.Rmd +++ b/Markdown/RSessionInfo.Rmd @@ -0,0 +1,141 @@ +─ 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 + 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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 diff --git a/server.R b/server.R index 7a4a6b290409f697a8a86156b0c9dd653d3667c7..e3c7e9cea3f9947f9428391f63efdeb10b5c88d2 100755 --- a/server.R +++ b/server.R @@ -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 )