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| + | [[Category:Software]] |
| + | = Overview = |
| + | A few rare variants tests (Li-Leal's CMC and Madsen-Browning's weighted method) are implemented in the logisitc regression framework using C++. |
| + | |
| + | The source code is located at wonderland:/home/youna/prj/RV/RV3Tests.v1/ |
| + | |
| + | The binary file is located at wonderland:/home/youna/prj/RV/RV3Tests.v1/executables/rvTests |
| + | |
| + | = Example = |
| + | |
| + | See a detailed [[example]] here. |
| + | |
| + | = Syntax = |
| + | |
| + | This software uses command line interface as follows |
| + | |
| + | RARE VARIANT ANALYSIS OPTIONS: |
| + | GENOTYPE : --genofile [pos.012], |
| + | --geneList [outGeneSorted.txt], --cutoff [0.010], |
| + | --collapseChoice [or] |
| + | PHENOTYPE : --phenofile [LDL.y.ID] |
| + | COVARIATES : --covConsider, --covfile [covFile.ID.2.txt] |
| + | PERMUTATION : --nPermute [10], --PermutationSeed [1] |
| + | GENE LEVEL TEST RESULT : --geneGlobalTestOut [globalPermuteSummary.txt], |
| + | --geneTestpvalueFile [geneTestPvalues.txt] |
| + | |
| + | |
| + | ;GENOTYPE |
| + | |
| + | ;--genofile: A genotype 012 matrix (.012 is the file) This file can be prepared by using the prepare012s |
| + | source code (wonderland:/home/youna/prj/RV/vcfReader.v1) |
| + | binary file (wonderland:/home/youna/prj/RV/vcfReader.v1/executables/prepare012s) |
| + | |
| + | Note: If you going to analyze nonsynonymous and stop annotated variants, |
| + | you should use Yanming's vcf annotation [http://genome.sph.umich.edu/wiki/VcfCodingSnps] on the vcf file. |
| + | |
| + | Data File PREPARATION |
| + | Input files : --vcf [LDL.test.vcf], --log [], --IDfile [] |
| + | Subsetting choices : --All |
| + | Output files : --outputPrefix [subsetGeno], |
| + | --outputGeneList [LDL.geneList.txt] |
| + | --vcf: Input vcf file |
| + | --log: This is the log file from Yanming's annotation output, we use this log to obtain the gene list |
| + | --IDfile specifies a file with one column of subject IDs to subject from the vcf file. |
| + | If it is not specified, then all subjects are included for the format conversion. |
| + | --All: specifies 1 to include all variants and 0 to include only nonsyn and stop annotated variants. |
| + | -- outputPrefix: Specify the prefix for the four output files which will be used in rvTests |
| + | *.012: A genotype matrix with subjects as rows and variant sites as columns. |
| + | *.012.pos: Chromosome and position numbers. |
| + | *.012.indv: Subject IDs. |
| + | *.012.frq: The frequency of the included variants. |
| + | --outputGeneList: Specify a file to store the gene list which will be used in rvTest. |
| + | The list file looks like this |
| + | 1 OR4F5 69090 70008 |
| + | 1 SAMD11 860529 871276 |
| + | 1 NOC2L 879583 893918 |
| + | 1 KLHL17 895966 901095 |
| + | 1 PLEKHN1 901876 910482 |
| + | 1 C1orf170 910578 912021 |
| + | |
| + | ;--geneList: This file is an output from prepare012s using the option --outputGeneList with columns as chromosome number, gene Name, start position, end position. There should be no header for this file. |
| + | |
| + | THE CHROMOSOME NUMBERS SHOULD BE NUMERICS!!!! 1 - chromosome 1, DO NOT USE chr1. |
| + | |
| + | ;--cutoff: This is the minor allele frequency, you can specify it as 0.01, 0.05 or etc. |
| + | ;--collapseChoice: Specify one of {or,sum,wt}. or: Li-Leal's CMC test, sum: Use the number of rare variants for each subject as the score, wt: Madeson-Browning's weighted rare variant score. |
| + | |
| + | ;PHENOTYPE |
| + | ;--phenofile: A file where the first column is subject ID and the second column is phenotype (0 or 1). |
| + | |
| + | ;COVARIATES |
| + | ;--covConsider: Default = 0, no covariate is considered. 1. covariate is considered. |
| + | ;--covfile: Covariate file with the first column as subject ID and the other columns are covariates needed to be considered in the model. |
| + | |
| + | ;PERMUTATION |
| + | ;--nPermute: Number of permutation for the evaluation of p values. |
| + | ;-- PermutationSeed: Default = 1. Can be changed to other numbers too. |
| + | |
| + | ;GENE LEVEL TEST RESULT: |
| + | ;--geneGlobalTestOut: This file stores the 5% and 95% quantiles of the p values for all the genes at each permutation |
| + | ;--geneTestPvalueFile: This file gives you the gene name, number of rare variants, count of variants in case/control and p values from the RV test specified by collapseChoice. |