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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?

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Don't know which file was used by cummeRbund for sample names but replacing q1,q2,q3 and q4 with Batis, Blue_silver, Chakwal_50 and Syn_22 for all the files in the directory containing cuffdiff output worked for me.

I used sed language for this as shown below:

sed -i 's/q4/Syn_22/g' *

Or more generally you can use

sed -i 's/sample_name_shown/sample_name_to_change/g' *

After that I deleted the sqlite object created by cummeRbund and again created this object using readCufflinks() in R. This time sample names are changed as desired:

samples(cuff)
sample_index sample_name sample_name parameter value
1            1       Batis        <NA>      <NA>  <NA>
2            2 Blue_silver        <NA>      <NA>  <NA>
3            3  Chakwal_50        <NA>      <NA>  <NA>
4            4      Syn_22        <NA>      <NA>  <NA>
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