multiple ampersand for SAS macro

When macro variables contain the name of another macro variable or pieces of names of other macro variables the resulting code will often contain two (or more!!) ampersands.

A Gibbles sampler for Hierarchical Bayes

hieracrh1<-function(nsims,x,tau,kstart){
bold<-1
clambda<-rep(0,(nsims+kstart))
cb<-rep(0,(nsims+kstart))
for(i in 1: (nsims+kstart))
{clambda[i]<-rgamma(1,shape=(x+1),scale=(bold/(bold+1)))
newy<-rgamma(1,shape=2,scale=(tau/(clambda[i]*tau+1)))
cb[i] <-1/newy
bold<-1/newy
}
gibbslambda<-clambda[(kstart+1):(nsims+kstart)]
gibbsb<-cb[(kstart+1):(nsims+kstart)]
out<-list(clambda=clambda, cb=cb,gibbslambda=gibbslambda,gibbsb= gibbsb)
return(out)
}

mean(hieracrh1(4000,6,0.04,1000)$gibbslambda)
mean(hieracrh1(4000,6,0.045,1000)$gibbslambda)
mean(hieracrh1(4000,6,0.05,1000)$gibbslambda)
mean(hieracrh1(4000,6,0.055,1000)$gibbslambda)
mean(hieracrh1(4000,6,0.06,1000)$gibbslambda)

Install R package from the source

install.packages("path\file", repos = NULL, type="source")

Where path_to_file would represent the full path and file name:

• On Windows it will look something like this: "C:\\RJSONIO_0.2-3.tar.gz".
• On UNIX it will look like this: "/home/blah/RJSONIO_0.2-3.tar.gz"

some public genetic data

ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/

https://www.broadinstitute.org/medical-and-population-genetics/hapmap-3

ftp://ftp.illumina.com/

user name:guest
password:illumina

 http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20181203_biallelic_SNV/

Manhattan Plot for GWAS

if(!require("ggplot2")) {
  print("Please install the ggplot plackage")
  ## install.packages('ggplot2', dep=T)
}
 
require(ggplot2)

d <- read.table("simulated_assoc.assoc",header=T)
d <- na.omit(d)

maxy <- 15
sig <- -log10(5e-8)

d$logp <- -log10(d$P)
d$x <- NA
ticks <- NULL
lastbase <- 0

order <- order(d$CHR,d$BP)
d <- d[order,]
d[d$logp > maxy,'logp'] <- maxy

numchrs <- length(unique(d$CHR))

for( i in unique(d$CHR) ) {
  if( i==1 ) {
    d[d$CHR==i,]$x <- d[d$CHR==i,]$BP
  } else {
    lastbase <- lastbase+tail(subset(d,CHR==i-1)$BP,1)
    d[d$CHR==i,]$x <- d[d$CHR==i,]$BP+lastbase
  }
  ticks <- c(ticks,d[d$CHR==i,]$x[floor(length(d[d$CHR==i,]$x)/2)+1])
}
ticklim <- c(min(d$x),max(d$x))

if(numchrs > 1) {
  cols <- rep(c("gray","black"),max(d$CHR))
} else {
  cols <- "gray"
}

if (maxy=="max") maxy=ceiling(max(d$logp)) else maxy=maxy
if (maxy<8) maxy=8

pdf("manhattan_plot.pdf")

plot <- qplot(x,logp,data=d,
              ylab=expression(-log[10](italic(p))) , colour=factor(CHR))
plot <- plot + scale_x_continuous(name="Chromosome",
                                  breaks=ticks,
                                  labels=(unique(d$CHR)))
plot <- plot + scale_y_continuous(limits=c(0,maxy),
                                  breaks=1:maxy)
plot <- plot + scale_colour_manual(values=cols)
plot <- plot + theme(legend.position="none")
plot <- plot + labs(title="Manhattan Plot")
plot <- plot + theme(panel.background=element_blank(),
                    panel.grid.minor=element_blank())


plot <- plot + geom_abline(intercept=sig,slope=0, col="black")

some commands for Ubuntu

1. cd /home/user/Download
2. sudo cp filename /usr/bin

If you want to copy a folder from your download then just add -r before cp command

sudo cp -r foldername /usr/bin

you can use mv command to move that file or folder

sudo mv filename /usr/bin

 3. awk: line 2: missing } near end of file

use  awk '{print  $1,$2,$4,$5}'

Correlations for hierarchical models