Noi:Quicklinks: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Noi
mNo edit summary
>Noi
mNo edit summary
Line 12: Line 12:
  par(new=TRUE)
  par(new=TRUE)
  plot(x, y2, ylim=range(c(y1,y2)), axes = FALSE, xlab = "", ylab = "")
  plot(x, y2, ylim=range(c(y1,y2)), axes = FALSE, xlab = "", ylab = "")
 
* Example of histogram plot, set log scale on Y-axis
A=read.table("10%FDR_allCpG-SNP-2MB_mQTL_CpG-SNP_distance2",sep="\t")
head(A)
B=abs(A$V4)/1000
h <- hist(B, breaks=2000, plot=FALSE)
pdf("SNP-CpG_distance_all_CpG.mQTL_log.pdf",height=7.5, width=10)
plot(h$mids, h$counts, log="y", type='h',main="all CpG mQTL", col="#104E8B",lwd=4, ylab="Frequency", xlab="Distance between SNPs and CpG sites (kb)", cex.lab=1.5)
axis(side = 1, at = seq(0,2000,250))
'''http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm'''<br>
'''http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm'''<br>
'''R:Data structure:''' http://www.statmethods.net/input/datatypes.html<br>
'''R:Data structure:''' http://www.statmethods.net/input/datatypes.html<br>

Revision as of 22:11, 28 September 2012

Link to calendar:[[1]]
Install R packages: install.packages("package_name")
SNP 134 data base : on genome-miner: /media/Ext4T/GenomeDB/HsGenome/snp134_snv.txt
genemapster address: nplongth@genemapster.dynamic.ucsd.edu

Triton

  • checkjob -v jobid = job diagnosis
  • gbalance -p zhang-lab = check credit balance of zhang-lab

R plotting

  • Multiple plots on the same axis
plot(x, y1, ylim=range(c(y1,y2)))
par(new=TRUE)
plot(x, y2, ylim=range(c(y1,y2)), axes = FALSE, xlab = "", ylab = "")
  • Example of histogram plot, set log scale on Y-axis
A=read.table("10%FDR_allCpG-SNP-2MB_mQTL_CpG-SNP_distance2",sep="\t")
head(A)
B=abs(A$V4)/1000
h <- hist(B, breaks=2000, plot=FALSE)
pdf("SNP-CpG_distance_all_CpG.mQTL_log.pdf",height=7.5, width=10)
plot(h$mids, h$counts, log="y", type='h',main="all CpG mQTL", col="#104E8B",lwd=4, ylab="Frequency", xlab="Distance between SNPs and CpG sites (kb)", cex.lab=1.5)
axis(side = 1, at = seq(0,2000,250))

http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm
R:Data structure: http://www.statmethods.net/input/datatypes.html
R: Graphic parameters, text & symbol size, plotting symbols, lines, colors, fonts, margins and graph size:http://www.statmethods.net/advgraphs/parameters.html
R: color chart:http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf
Multiple testing correction: MultipleTestCorrection_Agilent

Dinh:COMPUTATIONAL/bisReadMapper: http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh:COMPUTATIONAL/bisReadMapper
BEDtools and Table browser (to get annotated file)

Group: Genes and Gene Prediction Tracks
Track: RefSeq Genes
Table: RefGenes