sequence <- read.csv("~/Downloads/sequence.fasta", header=F)
View(sequence)
library(Ringo)
?annotationobject
?posToProbeAnno
probeAnno<-posToProbeAnno("121101_OysterV9_MG_meth.pos", genome="Pacific Oyster", microarrayPlatform="NimbleGen 121101 Oyster V9 MG meth")
source('~/.active-rstudio-document')
source.with.encoding('~/Documents/Macs folder UW/courses/FISH 560 multivariate/course materials/biostats.R', encoding='UTF-8')
probeAnno<-posToProbeAnno("121101_OysterV9_MG_meth.pos", genome="Pacific Oyster", microarrayPlatform="NimbleGen 121101 Oyster V9 MG meth")
setwd("/Volumes/web/bivalvia/array/nimblegen/designs_1of1")
probeAnno<-posToProbeAnno("121101_OysterV9_MG_meth.pos", genome="Pacific Oyster", microarrayPlatform="NimbleGen 121101 Oyster V9 MG meth")
probeAnno<-posToProbeAnno("121101_OysterV9_MG_meth.pos", genome="Pacific Oyster", microarrayPlatform="NimbleGen 121101 Oyster V9 MG meth")
?save
?posToProbeAnno
probeAnno<-posToProbeAnno("121101_OysterV9_MG_meth.pos", genome="Pacific Oyster", microarrayPlatform="NimbleGen 121101 Oyster V9 MG meth",verbose = FALSE)
save(probeAnno,file="121101_OysterV9_MG_meth.ProbeAnnotation_MG.rda")
head(probeAnno)
head(probeAnno)
install.packages('knitr', dependencies = TRUE)
library(knitr)
?knit
library(knitr)
update.packages(ask = FALSE, repos = 'http://cran.rstudio.org')
type = 'source')
install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.org'),
type = 'source')
install.packages("knitr", repos = c("http://rforge.net", "http://cran.rstudio.org"),
update.packages(ask = FALSE, repos = 'http://cran.rstudio.org')
install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.org'),
type = 'source')
library(Ringo)
?findChersOnSmoothed
install.packages("ChIPpeakAnno")
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")
?eprs
?exprs
??exprs
library(Ringo)
?exprs
setwd("/Volumes/web/bivalvia/array/Rstuff")