I want to analyze RNA seq data using R package cummeRbund. Using this package I have a problem changing sample names. When I run this command in cummeRbund
samples(cuff) sample_index sample_name sample_name parameter value 1 1 q1 <NA> <NA> <NA> 2 2 q2 <NA> <NA> <NA> 3 3 q3 <NA> <NA> <NA> 4 4 q4 <NA> <NA> <NA> 5 5 q5 <NA> <NA> <NA>
It shows q1,q2,q3,q4 and q5 as sample names for the five samples but I want to change the sample names and put following names for the samples Batis, Blue_silver, Chakwal_50, Local_white and Syn_22 for q1,q2,q3,q4 ad q5 respectively. To accomplish this I ran following command:
> samples(cuff) <- c("Batis", "Blue_silver","Chakwal_50","Local_white","Syn_22") Error in samples(cuff) <- c("Batis", "Blue_silver", "Chakwal_50", "Local_white", : could not find function "samples<-"
but this command gave error as shown above.
Also the BAM files have same names for all the samples as mentioned above.
How could I change the sample names to desired names in R using cummeRbund?
Or I need to re-run cuffdiff and change the names somewhere else?