Man pages for genMOSSplus
Application of MOSS algorithm to genome-wide association study (GWAS)
| ex2plink | Convert example dataset to Plink format |
| genMOSSplus-package | Application of MOSS algorithm to dense SNP array data |
| genos.clean | Removes badly predicted SNPs by MaCH |
| genos.clean.batch | Removes badly predicted SNPs by MaCH for all files |
| get.data.dims | Obtains matrix dimensions |
| get.file.copy | Copies files from one directory to another |
| MOSS.GWAS | A function implementing the MOSS algorithm for the analysis... |
| pre0.dir.create | Generate working subdirectory structure |
| pre1.plink2mach | Convert Plink to MaCH input format |
| pre1.plink2mach.batch | Convert Plink to MaCH input format for all files |
| pre2.remove.genos | Remove genos with many empty values |
| pre2.remove.genos.batch | Remove genos with many empty values for all files |
| pre3.call.mach | Call MaCH imputation with and without Hapmap |
| pre3.call.mach.batch | Call MaCH imputation with and without Hapmap |
| pre4.combine.case.control | Combine CASE and CONTROL files |
| pre4.combine.case.control.batch | Combine CASE and CONTROL files for all files |
| pre5.genos2numeric | Categorize genotype data into 3 levels |
| pre5.genos2numeric.batch | Categorize genotype data into 3 levels for each file |
| pre6.merge.genos | Combine geno files across all chromosomes |
| pre7.add.conf.var | Append confounding variables |
| pre7.add.conf.var.unix | Append confounding variables using Linux |
| pre8.split.train.test | Split dataset into TRAIN and TEST files |
| pre8.split.train.test.batch | Split dataset into TRAIN and TEST files for all files |
| run1.moss | Runs MOSS regression algorithm |
| tune1.subsets | Imputes dense map of SNPs on chromosome regions with MaCH |
