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

steps for simulation sample size

1. Write the statistical model mathematically.
2. Generate the sample according to the model with sample size N.
3. Fit the model, perform the test, and record the rejection or acceptance of hull hypothesis.
4. Repeat step 2 and 3 n (generally I used 5000) times.
5. Calculate the power by (# of rejections)/n.

6 If power is too higher, decrease sample size N, repeat 2 - 5. If power is too lower, increase sample size N, repeat 2 - 5.

number of basis fuction for spline regression

The number of basis function is n+d+1, where n is the number of (internal) knots, where d is the degree of the basis function.

R datasets

https://vincentarelbundock.github.io/Rdatasets/datasets.html