Commit 03a828eb by Mustafa Tekpinar

Updated prescott-scores-details.csv info in the docs.

parent e1284daa
...@@ -110,7 +110,27 @@ if you would like to use GnomAD v2.1.1, you should specify the version with '--g ...@@ -110,7 +110,27 @@ if you would like to use GnomAD v2.1.1, you should specify the version with '--g
The most important output is prescott-scores.csv file, which produces entire single point mutational landscape for the protein. The most important output is prescott-scores.csv file, which produces entire single point mutational landscape for the protein.
In addition, there is a file called prescott-scores-details.csv. The file contains all information about the points modulated by population In addition, there is a file called prescott-scores-details.csv. The file contains all information about the points modulated by population
information coming from gnomad file and non-modulated variants. information coming from gnomad file and non-modulated variants. Here are a few lines from the example
.. code:: bash
mutant,ESCOTT,protein,log10frequency,labels,position,PRESCOTT
M1V,0.27,MLH1_normPred_evolCombi,999.0,,1,0.27
M1W,0.36,MLH1_normPred_evolCombi,999.0,,1,0.36
M1Y,0.36,MLH1_normPred_evolCombi,999.0,,1,0.36
S2A,0.06,MLH1_normPred_evolCombi,-5.55059765214601,,2,0.06
There are seven fields in that file: mutant,ESCOTT,protein,log10frequency,labels,position,PRESCOTT.
Let's explain each field separately.
1. mutant: M1V
2. ESCOTT: A floating point ESCOTT score of the variant (0.27).
3. protein: This is a string derived from your input file name (MLH1_normPred_evolCombi).
4. log10frequency: If you gnomad file constains frequency information for this variant, you will have a value such as -5.55059765214601. When your gnomad file does not contain any frequency information for that variant, you will see 999.0 in that field.
5. labels: If your gnomad file constains 'Pathogenic', 'Pathogenic/Likely pathogenic' or 'Likely pathogenic' ClinVar labels, your labels field will be 1. If your gnomad file constains 'Benign', 'Benign/Likely benign' or 'Likely benign' ClinVar labels, your labels field will be 0. If there is not any Clinvar label, the field will remain empty.
6. position: An integer value clearly indicating amino acid position in your protein.
7. PRESCOTT: A floating point PRESCOTT score of the variant (0.27).
Finally, if you have both pathogenic and benign labels in the gnomad file, there will be a 'clinvar-vs-position.png' file showing how these labeled Finally, if you have both pathogenic and benign labels in the gnomad file, there will be a 'clinvar-vs-position.png' file showing how these labeled
variants are affected by population information. variants are affected by population information.
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