jnhutchinson

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table.sourceCode, tr.sourceCode, td.lineNumbers, td.sourceCode {
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table.sourceCode { width: 100%; }
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jnhutchinson

library(plyr)
library(Rsamtools)
library(GenomicRanges)
library(Biostrings)
library(knitr)

matcher <- function(pattern, x) {
  ind = gregexpr(pattern, x)[[1]]
  start = as.numeric(ind)
  end = start + attr(ind, "match.length")- 2

jnhutchinson

## 2012-05-08 - first draft
## 2012-05-14 - got rid of repetitive parts of script
## 				added RNA-seqQC prep
###jnhutchinson
###bash script to run tophat alignments for WP-rna-seq

###hard coded

#basedataDir	---untrimmed
#				---trimmed

jnhutchinson

source("http://bioconductor.org/biocLite.R") #adds bioconductor site as a package source
BiocLite(“pheatmap”) #downloads and install pheatmap package from bioconductor
library(pheatmap) #loads pheatmap package

install.packages(“RColorBrewer”) #donwnloads and installs a package with useful color themes 
Library(RColorBrewer) #load RcolorBrewer package

#LOAD DATA
data=read.delim(“KO-WT-OV-3way.sig.batch.exprs.xls”) #read in expression values for significantly correlated probesets
data=data[,1:6] #subsets data remove the gene symbols, names or EntrezIDs

jnhutchinson

library(XML)
address="Boston"
url = paste( "http://www.google.com/ig/api?weather=", URLencode(address), sep="" )
xml = xmlTreeParse(url, useInternalNodes=TRUE) # take a look at the xml output:
# Get the required informations:
condition=xpathSApply(xml,"//xml_api_reply/weather/current_conditions/condition",xmlGetAttr,"data")
temp_c=xpathSApply(xml,"//xml_api_reply/weather/current_conditions/temp_c",xmlGetAttr,"data")
humidity=xpathSApply(xml,"//xml_api_reply/weather/current_conditions/humidity",xmlGetAttr,"data")
cat( paste("The Weather in ", address, " is ", condition, ". The temperature is ", temp_c, "°C. Humidity is ", humidity, "%.") )

jnhutchinson

library(XML)
address="Boston"
url = paste( "http://www.google.com/ig/api?weather=", URLencode(address), sep="" )
xml = xmlTreeParse(url, useInternalNodes=TRUE) # take a look at the xml output:
# Get the required informations:
condition=xpathSApply(xml,"//xml_api_reply/weather/current_conditions/condition",xmlGetAttr,"data")
temp_c=xpathSApply(xml,"//xml_api_reply/weather/current_conditions/temp_c",xmlGetAttr,"data")
humidity=xpathSApply(xml,"//xml_api_reply/weather/current_conditions/humidity",xmlGetAttr,"data")
cat( paste("The Weather in ", address, " is ", condition, ". The temperature is ", temp_c, "°C. Humidity is ", humidity, "%.") )