opts_chunk$set(tidy=TRUE, cache=FALSE, highlight=TRUE, figalign="center", warning=FALSE, error=FALSE, message=FALSE, fig.height=11, fig.width=11)
library(ggplot2)
library(xtable)
Oliver Hofmann ohofmann
ohofmann
/ gist:2771492
Created
May 22, 2012 20:42
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| Try to de-convolute the array relationships by looking at the SNP | |
| # probes | |
| snpProbes <- grep('rs', fData(lumiData)$TargetID) | |
| betas <- estimateBeta(lumiData) | |
| betasSNP <- exprs(betas)[snpProbes, ] | |
| labels <- paste(pData(lumiData)$Subject, | |
| pData(lumiData)$sampleID, | |
| pData(lumiData)$Tissue, | |
| sep='_') |
ohofmann
/ gist: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: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: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" |
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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
/ 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) |
ohofmann
/ gist:2911187
Created
June 11, 2012 16:50
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| ### KNITR SETUP | |
| ```{r setup, echo=FALSE} | |
| opts_chunk$set(tidy=TRUE, cache=FALSE, highlight=TRUE, figalign="center", warning=FALSE, error=FALSE, message=FALSE, fig.height=11, fig.width=11) | |
| ``` | |
| ### EXAMPLE CHUNK | |
| ```{r libraries} | |
| library(ggplot2) | |
| library(xtable) |
ohofmann
/ gist:2911193
Created
June 11, 2012 16:50
ohofmann
/ gist:2911484
Created
June 11, 2012 17:36
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| library(getopt) | |
| options <- c('help', 'h', 0, 'logical', | |
| 'reads', 'r', 1, 'character', | |
| 'targets', 't', 1, 'character') | |
| opt = getopt(matrix(options, ncol=4, byrow=T)) | |
| # Help was asked for. | |
| if (!is.null(opt$help)) { |
ohofmann
/ gist:6e59d794757099fd154d
Created
June 20, 2014 18:41
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| # Create a vector of sex-specific positive control genes | |
| sex.symbols <- c("XIST","CYorf15A","DDX3Y","KDM5D","RPS4Y1","USP9Y","UTY"); | |
| sex.genes <- featureNames(dataset)[match(sex.symbols, fData(dataset)$Symbol)]; | |
| names(sex.genes) <- sex.symbols; | |
| sex.genes <- na.omit(sex.genes); | |
| # Draw stripcharts of expression of each sex-specific gene | |
| pdf.filename <- file.path(project.path, sprintf("%s_sex_stripcharts.pdf", project.prefix)); | |
| if (!file.exists(pdf.filename)) { | |
| pdf(pdf.filename, width=11, height=8.5); |