Note: The most recent implementation of the model can be found as part of the
SHazaM package in the immcantation suite (
http://www.immcantation.org)
Download
VERSION
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July 26, 2013
Version 0.1
REQUIREMENTS
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R
DIRECTIONS
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* Baseline_Functions.r
Contains all the functions needed for the Baseline_Main.r and SHMulation.r
* Mutability.r
The main program that builds the SF5 mutability model. You can run the program from the command line using RScript:
e.g.
Rscript mutability.r [model] [multipleMuation] [seqWithStops] [clonal] [fixIndels] [inputFilePath] [outputPath] [ouputID] [MinMu] [MaxMu]
+ model:
0 = Use ALL mutations to build model
1 = Use only SILENT mutations to build model
+ multipleMuation:
0 = Treat independently
1 = Ignore codons with multiple mutations
+ seqWithStops
0 = Do nothing
1 = Remove stop mutations
2 = Include only sequences with stop
3 = Include only sequences without stop
+ clonal:
0 = Sequences are all independent
1 = Treat each germline group as a single, independent clone.
+ fixIndels:
0 = Ignore all sequences with insertion/deletions
1 = Attempt to correct the indels by adding an "N" to the germline (insertion) or the input (deletion), at the position of the indel.
+ inputFilePath:
Full path to the input file
+ outputPath:
Full path to output directory
+ outputID:
ID to name output files
+ MinMu:
Minimum number of mutations a sequence needs to have to be included in the analysis
+ MaxMu:
Maximum number of mutations a sequence needs to have to be included in the analysis
* Substitution.r
The main program that builds the SF5 substitution model. You can run the program from the command line using RScript:
e.g.
Rscript Substitution.r [model] [multipleMuation] [seqWithStops] [clonal] [fixIndels] [inputFilePath] [outputPath] [ouputID] [MinMu] [MaxMu]
+ model:
0 = Use ALL mutations to build model
1 = Use only SILENT mutations to build model
+ multipleMuation:
0 = Treat independently
1 = Ignore codons with multiple mutations
+ seqWithStops
0 = Do nothing
1 = Remove stop mutations
2 = Include only sequences with stop
3 = Include only sequences without stop
+ clonal:
0 = Sequences are all independent
1 = Treat each germline group as a single, independent clone.
+ fixIndels:
0 = Ignore all sequences with insertion/deletions
1 = Attempt to correct the indels by adding an "N" to the germline (insertion) or the input (deletion), at the position of the indel.
+ inputFilePath:
Full path to the input file
+ outputPath:
Full path to output directory
+ outputID:
ID to name output files
+ MinMu:
Minimum number of mutations a sequence needs to have to be included in the analysis
+ MaxMu:
Maximum number of mutations a sequence needs to have to be included in the analysis
Change Log
July 26, 2013
Version 0.1
