MSI score Plot

[Jemkon]

Hello,

I have got the output files for tumor only BAMs. I would like to run Plot.R script. But I dont know which file I should use as input to Plot.R.

Here are 3 my outfiles:
tumorBam.MSI
tumorBaM.MSI_dis
tumorBam.MSI_somatic

Many thanks,

[ZhaoDanOnGitHub]

Hello,

The function of drawing is for the sample group, not for a single sample.
You can refer to the example in the test folder: msi_score_and_status_list and msi_score_only_list. Each line is a sample of msicore and status or msiscore only. Msiscore is obtained form tumorBam.MSI.
For example, there are two samlpes: sample_1 and sample_2. We will get 3 outfiles for each sample. For sample_1, we will get sample_1_output, sample_1_output_dis, sample_1_output_somatic. And for sample_2, 3 outfiles are sample_2_output, sample_2_output_dis and sample_2_output_somatic.
For sample_1, outfile sample_1_output is as follow:
Total_Number_of_Sites Number_of_Somatic_Sites %
12015 3425 28.51
For samlple_2, outfile sample_2_output is as follow:
Total_Number_of_Sites Number_of_Somatic_Sites %
9219 33 0.36
Then we extract msiscores from sample_1 and sample_2. If you have MSI status, msi_score_and _status_list file is as follow:
MSI 28.51
MSS 0.36
If you don’t have MSI status, msi_score_only_list is as follow:
28.51
0.36
You can use msi_score_and_status_list or msi_score_onlu_list as input for Plot.R.

Thanks

[Jemkon]

Hi Many thanks for the detailed info. If I use -r option to specify the region for msi, then it will look for only 1 window and if it found msi site then the score will be 100%. All samples will have 100 msi score and the distribution will looks the same. How do i classify them?

Many thanks.