fetchSignal {SAGx} | R Documentation |
Fetch FILENAME, PROBESET, SIGNAL and ABS_CALL from the GATC database
fetchSignal(experiment="AZ33 ALI", channel, chip="HG_U95Av2")
experiment |
The name of the experiment corresponding to an individual chip |
channel |
The channel to the database |
chip |
the chip type |
dataframe with columns
Ported to R by Per Broberg. Original Oracle code by Petter Hallgren, with input from Petra Johansson.
## Not run: # Do not run example 1. Fetch Probeset, Signal, ABS_CALL and CHIP for one sample. library(RODBC) (channel<-odbcConnect("DSN",uid="USERID",pwd="PASSWORD")) ali.data <-fetchSignal(experiment="AZ33 ALI", channel, chip="hg_u95a") colnames(ali.data) #[1] "FILENAME" "PROBESET" "SIGNAL" "ABS_CALL" "CHIP" # Do not run example 2 t1 <- paste("select q1.name as name from experiment q1, physical_chip q2, chip_design q3") t2 <- paste("where q1.physical_chip_id=q2.id and q3.id=q2.design_id and ") t3 <- paste("upper(q1.name) like ' Ids <- sqlQuery(channel,paste(t1,t2,t3) ) # fetch Signal from GATC corresponding to the U95A chip for all samples in experiment. # tmp <- apply(Ids,1,toupper) probes <- data.frame(fetchSignal(experiment=tmp[1],channel, chip="hg_u95a")[,"PROBESET"]) test <- matrix(nrow=nrow(as.data.frame(probes)),ncol=nrow(Ids)) for(i in 1:nrow(as.data.frame(tmp))){ test[,i] <- fetchSignal(experiment=tmp[i],channel, chip="hg_u95a")[,"SIGNAL"] } codes <- data.frame(apply(Ids,1,code<-function(x) substr(x,1,5))) colnames(test) <- as.character(t(codes)) test <- test[,order(colnames(test))] ## End(Not run)