Hello, I have been trying to use the Immune_repertoire portion of the RIMA pipeline to calculate SHM statistics for TRUST4 output mouse data (that has not otherwise been processed through the RIMA pipeline).
Rscript src/immune_repertoire/trust4_bcr_process.R --cdr3 C1.processed.txt -s test -o out
However, when I run trust4_bcr_process.R, the program fails with
[1] "Saving SHM results ..."
Error in if (is.na(sample_bcr_cluster)) { : the condition has length > 1
Execution halted
Commenting out that section of the code shown below allows it to run to completion, but I am worried about the effect on the validity of the data analysis.
} else if (is.na(sample_bcr_cluster)) {
ss.ratio <- NULL
Do you have any suggestions for fixing this?
Also, what is the actual statistic being calculated for the SHMRatio output? I am trying to make sure I understand what the values being outputted mean.
Thank you for your time and help, and happy holidays.
Hello, I have been trying to use the Immune_repertoire portion of the RIMA pipeline to calculate SHM statistics for TRUST4 output mouse data (that has not otherwise been processed through the RIMA pipeline).
However, when I run trust4_bcr_process.R, the program fails with
Commenting out that section of the code shown below allows it to run to completion, but I am worried about the effect on the validity of the data analysis.
Do you have any suggestions for fixing this?
Also, what is the actual statistic being calculated for the SHMRatio output? I am trying to make sure I understand what the values being outputted mean.
Thank you for your time and help, and happy holidays.