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