markhaser.blogg.se - Cmh constructor 9 setup file

gcdhBmCreate: Create a big.matrix under specified GCDH tag.

FilePath-class: An S4 class to represent a file path.

filePath: Constructor for FilePath class.

file.create2: Create file if it does not already exist.

fidIid: FID and IID columns from fam file.

famCorrectTypes: Correct types of fam ame.evalFile: Eval R expressions from a file.eprint: Print quoted expression then its value.dir.create2: Create directory if it does not already exist.datToVec: Extract one row or column of a data frame as a vector.cytoband: Find cytoband at a given position.covarNames: Get covariate names of a GWAS.correctTypes_methods: Convert columns of a data frame to certain types.correctDesc: Correct description of big.matrix.contrastPlot: Produce contrast Manhattan plot.contrastData: Prepare data for 'contrastPlot'.connectSnpPair: Annotate a pair of SNPs in the contrast Manhattan plot.

collenv: An environment for storing CollapsABEL package local.

collClear: Clear up CollapsABEL workspace.

collapseMat: Collapse two genotype matrices, column by column.CollapsABEL: CollapsABEL: an R library for detecting compound heterozygote.colCors: Correlation coefficient of column-pairs of two data frames.colClasses: Get classes of columns of a ame.cmh: Contrast Manhattan plot the simple way.checkFileExist: Stop when any file does not exist.charify: Convert certain columns of a ame to character type.changeByMap: Transform a vector by a mapping.bytesSnp: Get number of bytes used by each SNP.bmFilepath: Get the big.matrix file path according to GCDH task tag.bmFilename: Generate a big.matrix filename (.bin or.bmConvertFun: Conversion function to use when appending values to a.bmAttachBin: Attach a big.matrix by its bin filename.bmAddCol: Add column(s) to an existing big.matrix.binPhe: Check whether phenotype of a GWAS is binary.bimCorrectTypes: Correct types of bim ame.bedSizeCorrect: Check whether bed file is of correct size.baseName: Basename of a FilePath object.assocFilter: Filter a PlGwasC object by the results of a 'plink –assoc'.asBigMatrix: Coerce an R vector/matrix/ame into a big.matrix.