MVP.Data {rMVP} | R Documentation |
MVP.Data: To prepare data for MVP package Author: Xiaolei Liu, Lilin Yin and Haohao Zhang Build date: Aug 30, 2016 Last update: Sep 12, 2018
MVP.Data(fileMVP = NULL, fileVCF = NULL, fileHMP = NULL, fileBed = NULL, fileNum = NULL, fileMap = NULL, filePhe = NULL, fileInd = NULL, fileKin = NULL, filePC = NULL, out = "mvp", sep.num = "\t", auto_transpose = TRUE, sep.map = "\t", sep.phe = "\t", sep.kin = "\t", sep.pc = "\t", type.geno = "char", pheno_cols = NULL, SNP.impute = "Major", maxLine = 10000, priority = "speed", pcs.keep = 5, verbose = TRUE, ncpus = NULL, ...)
fileMVP |
Genotype in MVP format |
fileVCF |
Genotype in VCF format |
fileHMP |
Genotype in hapmap format |
fileBed |
Genotype in PLINK binary format |
fileNum |
Genotype in numeric format; pure 0, 1, 2 matrix; m * n, m is marker size, n is sample size |
fileMap |
SNP map information, there are three columns, including SNP_ID, Chromosome, and Position |
filePhe |
Phenotype, the first column is taxa name, the subsequent columns are traits |
fileInd |
Individual name file |
fileKin |
Kinship that represents relationship among individuals, n * n matrix, n is sample size |
filePC |
Principal components, n*npc, n is sample size, npc is number of top columns of principal components |
out |
prefix of output file name |
sep.num |
seperator for numeric file. |
auto_transpose |
Whether to automatically transpose numeric genotypes, the default is True, which will identify the most one of the rows or columns as a marker, If set to False, the row represents the marker and the column represents the individual. |
sep.map |
seperator for map file. |
sep.phe |
seperator for phenotype file. |
sep.kin |
seperator for Kinship file. |
sep.pc |
seperator for PC file. |
type.geno |
type parameter in bigmemory, genotype data. The default is char, it is highly recommended *NOT* to modify this parameter. |
pheno_cols |
Extract which columns of the phenotype file (including individual IDs) |
SNP.impute |
"Left", "Middle", "Right", or NULL for skip impute. |
maxLine |
number of SNPs, only used for saving memory when calculate kinship matrix |
priority |
"speed" or "memory" |
pcs.keep |
how many PCs to keep |
verbose |
whether to print detail. |
ncpus |
The number of threads used, if NULL, (logical core number - 1) is automatically used |
... |
Compatible with DEPRECATED parameters. |
NULL Output files: genotype.desc, genotype.bin: genotype file in bigmemory format phenotype.phe: ordered phenotype file, same taxa order with genotype file map.map: SNP information k.desc, k.bin: Kinship matrix in bigmemory format pc.desc, pc.bin: PC matrix in bigmemory format Requirement: fileHMP, fileBed, and fileNum can not input at the same time
bfilePath <- system.file("extdata", "02_bfile", "mvp", package = "rMVP") opts <- options(rMVP.OutputLog2File = FALSE) MVP.Data(fileBed=bfilePath, out=file.path(tempdir(), "rMVP.test"), ncpus=1) options(opts)