Oliver Hofmann ohofmann
ohofmann
/ gist:2911187
Created
June 11, 2012 16:50
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| ### KNITR SETUP | |
| ```{r setup, echo=FALSE} | |
| opts_chunk$set(tidy=TRUE, cache=FALSE, highlight=TRUE, figalign="center", warning=FALSE, error=FALSE, message=FALSE, fig.height=11, fig.width=11) | |
| ``` | |
| ### EXAMPLE CHUNK | |
| ```{r libraries} | |
| library(ggplot2) | |
| library(xtable) |
ohofmann
/ knitr.rmd
Created
June 11, 2012 16:49
— forked from jnhutchinson/knitr.rmd
example knitr.r
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| ### KNITR SETUP | |
| ```{r setup, echo=FALSE} | |
| opts_chunk$set(tidy=TRUE, cache=FALSE, highlight=TRUE, figalign="center", warning=FALSE, error=FALSE, message=FALSE, fig.height=11, fig.width=11) | |
| ``` | |
| ### EXAMPLE CHUNK | |
| ```{r libraries} | |
| library(ggplot2) | |
| library(xtable) |
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| about title: "Variant filtering from amplicon data" | |
| PICARD_HOME="/n/HSPH/local/share/java/picard/" | |
| GATK_HOME="/n/HSPH/local/share/java/gatk/" | |
| SNPEFF_HOME="/n/HSPH/local/share/java/snpeff/" | |
| SNPEFF_CONF="/n/HSPH/local/share/java/snpeff/snpEff.config" | |
| HG19="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/seq/hg19.fa" | |
| HG19CHR='../chrTargets.bed' | |
| TARGETS="../exonTargetsSorted.bed" | |
| DBSNP132="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/variation/dbsnp_132.vcf" |
ohofmann
/ gist:2870474
Created
June 4, 2012 19:54
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| about title: "Variant filtering from amplicon data" | |
| PICARD_HOME="/n/HSPH/local/share/java/picard/" | |
| GATK_HOME="/n/HSPH/local/share/java/gatk/" | |
| SNPEFF_HOME="/n/HSPH/local/share/java/snpeff/" | |
| SNPEFF_CONF="/n/HSPH/local/share/java/snpeff/snpEff.config" | |
| HG19="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/seq/hg19.fa" | |
| HG19CHR='../chrTargets.bed' | |
| TARGETS="../exonTargetsSorted.bed" | |
| DBSNP132="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/variation/dbsnp_132.vcf" |
ohofmann
/ gist:2868830
Created
June 4, 2012 14:47
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| about title: "Variant filtering from amplicon data" | |
| PICARD_HOME="/n/HSPH/local/share/java/picard/" | |
| GATK_HOME="/n/HSPH/local/share/java/gatk/" | |
| SNPEFF_HOME="/n/HSPH/local/share/java/snpeff/" | |
| SNPEFF_CONF="/n/HSPH/local/share/java/snpeff/snpEff.config" | |
| HG19="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/seq/hg19.fa" | |
| HG19CHR='../chrTargets.bed' | |
| TARGETS="../exonTargetsSorted.bed" | |
| DBSNP132="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/variation/dbsnp_132.vcf" |
ohofmann
/ gist:2868826
Created
June 4, 2012 14:46
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| about title: "Variant filtering from amplicon data" | |
| PICARD_HOME="/n/HSPH/local/share/java/picard/" | |
| GATK_HOME="/n/HSPH/local/share/java/gatk/" | |
| SNPEFF_HOME="/n/HSPH/local/share/java/snpeff/" | |
| SNPEFF_CONF="/n/HSPH/local/share/java/snpeff/snpEff.config" | |
| HG19="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/seq/hg19.fa" | |
| HG19CHR='../chrTargets.bed' | |
| TARGETS="../exonTargetsSorted.bed" | |
| DBSNP132="/n/scratch00/hsph/biodata/genomes/Hsapiens/hg19/variation/dbsnp_132.vcf" |
ohofmann
/ gist:2771492
Created
May 22, 2012 20:42
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| Try to de-convolute the array relationships by looking at the SNP | |
| # probes | |
| snpProbes <- grep('rs', fData(lumiData)$TargetID) | |
| betas <- estimateBeta(lumiData) | |
| betasSNP <- exprs(betas)[snpProbes, ] | |
| labels <- paste(pData(lumiData)$Subject, | |
| pData(lumiData)$sampleID, | |
| pData(lumiData)$Tissue, | |
| sep='_') |
ohofmann
/ gist:2771491
Created
May 22, 2012 20:41
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| # Start with basic quality controls from lumi, highlight | |
| # samples by tissue information, also extract gender information | |
| colors <- brewer.pal(3, 'Set1') | |
| tissues <- pData(lumiData)$Tissue | |
| gender <- pData(lumiData)$Sex | |
| # Basic sample relations | |
| pdf('sampleRelations_mds_0.1_withRedos.pdf') | |
| plotSampleRelation(lumiData, method='mds', cv.Th=0.1, col=colors[tissues]) | |
| dev.off() |
ohofmann
/ gist:2433014
Created
April 21, 2012 01:00
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| library(ReadqPCR) | |
| library(NormqPCR) | |
| library(pheatmap) | |
| library(RColorBrewer) | |
| library(ggplot2) | |
| ###################################################################### | |
| # Setup | |
| ###################################################################### | |
| # Pairwise correlations |
ohofmann
/ gist:2433005
Created
April 21, 2012 00:55
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| library(simpleaffy) | |
| library(mouse430a2.db) | |
| library(arrayQualityMetrics) | |
| library(RColorBrewer) | |
| library(pheatmap) | |
| #library(pathprint) | |
| #library(ggplot2) | |
| #library(ggdendro) | |
| #library("AnnotationDbi") |