Man pages for CollapsABEL
Generalized CDH (GCDH) Analysis

alphaNumericAlpha-numeric characters
asBigMatrixCoerce an R vector/matrix/data.frame into a big.matrix
assocFilterFilter a PlGwasC object by the results of a 'plink –assoc'...
baseNameBasename of a FilePath object
bedcollrShift bed files
bedSizeCorrectCheck whether bed file is of correct size
bimCorrectTypesCorrect types of bim data.frame
bin2DescFilenameConvert a .bin filename to a .desc filename
binPheCheck whether phenotype of a GWAS is binary
bmAddColAdd column(s) to an existing big.matrix
bmAttachBinAttach a big.matrix by its bin filename
bmConvertFunConversion function to use when appending values to a...
bmFilenameGenerate a big.matrix filename (.bin or .desc)
bmFilepathGet the big.matrix file path according to GCDH task tag
bytesSnpGet number of bytes used by each SNP.
changeByMapTransform a vector by a mapping
charifyConvert certain columns of a data.frame to character type
checkFileExistStop when any file does not exist
chExtChange extension names
cmhContrast Manhattan plot the simple way
colClassesGet classes of columns of a data.frame
colCorsCorrelation coefficient of column-pairs of two data frames
CollapsABELCollapsABEL: an R library for detecting compound heterozygote...
collapseCollpase genotypes
collapseMatCollapse two genotype matrices, column by column
collClearClear up CollapsABEL workspace
collenvAn environment for storing CollapsABEL package local...
connectSnpPairAnnotate a pair of SNPs in the contrast Manhattan plot
contrastDataPrepare data for 'contrastPlot'
contrastPlotProduce contrast Manhattan plot
correctDescCorrect description of big.matrix
correctTypes_methodsConvert columns of a data frame to certain types
covarNamesGet covariate names of a GWAS
cytobandFind cytoband at a given position
datToVecExtract one row or column of a data frame as a vector
desc2BinFilenameConvert a .desc filename to a .bin filename
dir.create2Create directory if it does not already exist
dirNameDirectory name of a file path
eprintPrint quoted expression then its value
evalFileEval R expressions from a file.
famCorrectTypesCorrect types of fam data.frame
fidIidFID and IID columns from fam file
file.create2Create file if it does not already exist
filePathConstructor for FilePath class
FilePath-classAn S4 class to represent a file path
fileSizeGet file size
gcdhBmCreateCreate a big.matrix under specified GCDH tag
gcdhDirCreate GCDH task directories by tag
gcdhPowerGCDH power analysis
gcdhRegionRun GCDH over a region
gcdhReportGenerate a report from a GCDH run
getHaploInfer haplotypes for a pair of SNPs
getHaplosInferring haplotypes from two genotype data frames, and join...
getOrElse-operatorDefault value for expression.
getQueryGet query results from a SQLite database
getr2Estimate percentage of variation explained
glm2GLM with arbitrary column names
glmIterPerform glm iteratively through a number of independent...
gwasDatRead genotype and phenotype data into R
gwasDirGWAS results directory of a certain GWAS scan
gwasLogPlink log fie
gwasOutGWAS output file name
gwasOutStemPlink output filename
gwasRInvoke a GWAS in R
gwasRDSGet RDS file path of a PlGwasC object
head2Head and tail in two dimensions
headPheRead first n lines of a phenotype file
isBinaryCheck whether a trait is binary
isS4ClassCheck whether an S4 object is of a certain class
isSetupCheck if a directory containing .bed .fam and .bim files is...
isSetupRbedCheck if an RbedInfoC object is properly set up
isSQLite3Check whether a file is a SQLite3 database.
lagDistanceDistance with lag
lenCheckCheck each element of a list has expected length Give a...
listEqualCheck equality of two lists
listGwasTagsList GWAS or GCDH tags
loadGwasLoad PlGwasC object by tag, from the RDS file
makePheGenerate phenotype file from a fam file
manhattanDataPrepare data for Manhattan plot.
manhattanPlotProduce Manhattan plot
nIndivApprPlGet apparent number of individuals
nIndivPlGet number of individuals
nonExistentFilesNon-existent files from a vector of filenames
nSnpPlGet number of SNPs.
numVectorSQLReprString representation of a numeric vector for SQLite...
permutePhePermute a phenotype file
plGwasConstructor for PlGwasC class
PlGwasC-classAn S4 class representing info about GWAS on plink files
plInfoConstructor for PlInfoC class
PlInfoC-classAn S4 class representing info about plink files
plinkrA wrapper for plink
plTrimTrim plink files
qqQQ plot of one p-value vector
qq2QQ plot of two p-value vector
qqmultiQQ plot of multiple p-value vectors
randNormDatGenerate a m by n data.frame from normal distribution
randomStringGenerate a single alpha-numeric random string
randomStringsGenerate random strings
rbedInfoConstructor of RbedInfoC class
RbedInfoC-classS4 class for necessary info to read a bed file into R
readAssocRead PLINK .assoc files
readBedRead genotypes from PLINK bed file into R
readBimRead plink .bim files
readBmBinRead columns into an R matrix from a big.matrix .bin file
readDescRead big.matrix .desc file
readFamRead plink .fam files
readFunFactoryGenerate read_fun for ReadInfo class
readGwasOutRead GWAS output from plink If the GWAS is finished, returns...
readInfoReadInfo constructor
ReadInfo-classAn S4 class to represent information about a...
readLiteralRead a file literally (all columns as character)
readLogisticRead PLINK logistic regression output files.
readPheRead phenotype file
read.phe.tableRead phenotype file
readPlinkOutRead plink output files
readQassocRead .qassoc files
realBedSizeFile size of bed file
removeTagRemove GWAS results by tag
reprClassesRepresent classes of a data.frame in a character vector
rmFilesByStemRemove files by matching the starting part
runGcdhRun GCDH analysis
runGwasRun a GWAS
runTypeIRun simulations to control type-I error
saveDescSave big.matrix description object to disk
sendQuerySend query to SQLite database
setOptModelSet analysis model
setupSetup up a directory containing plink files
setupRbedSetup an RbedInfoC object
shiftBedShift bed files
shiftedStemAdd a "shift" suffix to a stem
slurpRead a text file into a single string
snpPosRetrive SNP positions from UCSU database
snpRowIdGet row number of SNPs from their names
spitWrite strings to a file
sqliteFilePlSQLite file of a PlInfoC object
stopFormatStop with format string
strConcatConcatenate a vector of strings
strVectorReprString Representation of a character vector
strVectorSQLReprString representation of a character vector for SQLite...
systemFormatCall system command with format string
theoBedSizeTheoretical size of bed file
validPheValidate a phenotype file
write.phe.tableWrite a phenotype data.frame to file
CollapsABEL documentation built on May 1, 2019, 7:28 p.m.