CollapsABEL: Generalized CDH (GCDH) Analysis
Version 0.10.11

Implements a generalized version of the CDH test ( and ) for detecting compound heterozygosity on a genome-wide level, due to usage of generalized linear models it allows flexible analysis of binary and continuous traits with covariates.

AuthorKaiyin Zhong, Fan Liu
Date of publication2016-12-11 20:35:07
MaintainerKaiyin Zhong <kindlychung@gmail.com>
LicenseGPL-3
Version0.10.11
URL https://bitbucket.org/kindlychung/collapsabel2/overview
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("CollapsABEL")

Popular man pages

asBigMatrix: Coerce an R vector/matrix/data.frame into a big.matrix
assocFilter: Filter a PlGwasC object by the results of a 'plink –assoc'...
nSnpPl: Get number of SNPs.
plinkr: A wrapper for plink
readBed: Read genotypes from PLINK bed file into R
readPlinkOut: Read plink output files
runTypeI: Run simulations to control type-I error
See all...

All man pages Function index File listing

Man pages

alphaNumeric: Alpha-numeric characters
asBigMatrix: Coerce an R vector/matrix/data.frame into a big.matrix
assocFilter: Filter a PlGwasC object by the results of a 'plink –assoc'...
baseName: Basename of a FilePath object
bedcollr: Shift bed files
bedSizeCorrect: Check whether bed file is of correct size
bimCorrectTypes: Correct types of bim data.frame
bin2DescFilename: Convert a .bin filename to a .desc filename
binPhe: Check whether phenotype of a GWAS is binary
bmAddCol: Add column(s) to an existing big.matrix
bmAttachBin: Attach a big.matrix by its bin filename
bmConvertFun: Conversion function to use when appending values to a...
bmFilename: Generate a big.matrix filename (.bin or .desc)
bmFilepath: Get the big.matrix file path according to GCDH task tag
bytesSnp: Get number of bytes used by each SNP.
changeByMap: Transform a vector by a mapping
charify: Convert certain columns of a data.frame to character type
checkFileExist: Stop when any file does not exist
chExt: Change extension names
cmh: Contrast Manhattan plot the simple way
colClasses: Get classes of columns of a data.frame
colCors: Correlation coefficient of column-pairs of two data frames
CollapsABEL: CollapsABEL: an R library for detecting compound heterozygote...
collapse: Collpase genotypes
collapseMat: Collapse two genotype matrices, column by column
collClear: Clear up CollapsABEL workspace
collenv: An environment for storing CollapsABEL package local...
connectSnpPair: Annotate a pair of SNPs in the contrast Manhattan plot
contrastData: Prepare data for 'contrastPlot'
contrastPlot: Produce contrast Manhattan plot
correctDesc: Correct description of big.matrix
correctTypes_methods: Convert columns of a data frame to certain types
covarNames: Get covariate names of a GWAS
cytoband: Find cytoband at a given position
datToVec: Extract one row or column of a data frame as a vector
desc2BinFilename: Convert a .desc filename to a .bin filename
dir.create2: Create directory if it does not already exist
dirName: Directory name of a file path
eprint: Print quoted expression then its value
evalFile: Eval R expressions from a file.
famCorrectTypes: Correct types of fam data.frame
fidIid: FID and IID columns from fam file
file.create2: Create file if it does not already exist
filePath: Constructor for FilePath class
FilePath-class: An S4 class to represent a file path
fileSize: Get file size
gcdhBmCreate: Create a big.matrix under specified GCDH tag
gcdhDir: Create GCDH task directories by tag
gcdhPower: GCDH power analysis
gcdhRegion: Run GCDH over a region
gcdhReport: Generate a report from a GCDH run
getHaplo: Infer haplotypes for a pair of SNPs
getHaplos: Inferring haplotypes from two genotype data frames, and join...
getOrElse-operator: Default value for expression.
getQuery: Get query results from a SQLite database
getr2: Estimate percentage of variation explained
glm2: GLM with arbitrary column names
glmIter: Perform glm iteratively through a number of independent...
gwasDat: Read genotype and phenotype data into R
gwasDir: GWAS results directory of a certain GWAS scan
gwasLog: Plink log fie
gwasOut: GWAS output file name
gwasOutStem: Plink output filename
gwasR: Invoke a GWAS in R
gwasRDS: Get RDS file path of a PlGwasC object
head2: Head and tail in two dimensions
headPhe: Read first n lines of a phenotype file
isBinary: Check whether a trait is binary
isS4Class: Check whether an S4 object is of a certain class
isSetup: Check if a directory containing .bed .fam and .bim files is...
isSetupRbed: Check if an RbedInfoC object is properly set up
isSQLite3: Check whether a file is a SQLite3 database.
lagDistance: Distance with lag
lenCheck: Check each element of a list has expected length Give a...
listEqual: Check equality of two lists
listGwasTags: List GWAS or GCDH tags
loadGwas: Load PlGwasC object by tag, from the RDS file
makePhe: Generate phenotype file from a fam file
manhattanData: Prepare data for Manhattan plot.
manhattanPlot: Produce Manhattan plot
nIndivApprPl: Get apparent number of individuals
nIndivPl: Get number of individuals
nonExistentFiles: Non-existent files from a vector of filenames
nSnpPl: Get number of SNPs.
numVectorSQLRepr: String representation of a numeric vector for SQLite...
permutePhe: Permute a phenotype file
plGwas: Constructor for PlGwasC class
PlGwasC-class: An S4 class representing info about GWAS on plink files
plInfo: Constructor for PlInfoC class
PlInfoC-class: An S4 class representing info about plink files
plinkr: A wrapper for plink
plTrim: Trim plink files
qq: QQ plot of one p-value vector
qq2: QQ plot of two p-value vector
qqmulti: QQ plot of multiple p-value vectors
randNormDat: Generate a m by n data.frame from normal distribution
randomString: Generate a single alpha-numeric random string
randomStrings: Generate random strings
rbedInfo: Constructor of RbedInfoC class
RbedInfoC-class: S4 class for necessary info to read a bed file into R
readAssoc: Read PLINK .assoc files
readBed: Read genotypes from PLINK bed file into R
readBim: Read plink .bim files
readBmBin: Read columns into an R matrix from a big.matrix .bin file
readDesc: Read big.matrix .desc file
readFam: Read plink .fam files
readFunFactory: Generate read_fun for ReadInfo class
readGwasOut: Read GWAS output from plink If the GWAS is finished, returns...
readInfo: ReadInfo constructor
ReadInfo-class: An S4 class to represent information about a...
readLiteral: Read a file literally (all columns as character)
readLogistic: Read PLINK logistic regression output files.
readPhe: Read phenotype file
read.phe.table: Read phenotype file
readPlinkOut: Read plink output files
readQassoc: Read .qassoc files
realBedSize: File size of bed file
removeTag: Remove GWAS results by tag
reprClasses: Represent classes of a data.frame in a character vector
rmFilesByStem: Remove files by matching the starting part
runGcdh: Run GCDH analysis
runGwas: Run a GWAS
runTypeI: Run simulations to control type-I error
saveDesc: Save big.matrix description object to disk
sendQuery: Send query to SQLite database
setOptModel: Set analysis model
setup: Setup up a directory containing plink files
setupRbed: Setup an RbedInfoC object
shiftBed: Shift bed files
shiftedStem: Add a "shift" suffix to a stem
slurp: Read a text file into a single string
snpPos: Retrive SNP positions from UCSU database
snpRowId: Get row number of SNPs from their names
spit: Write strings to a file
sqliteFilePl: SQLite file of a PlInfoC object
stopFormat: Stop with format string
strConcat: Concatenate a vector of strings
strVectorRepr: String Representation of a character vector
strVectorSQLRepr: String representation of a character vector for SQLite...
systemFormat: Call system command with format string
theoBedSize: Theoretical size of bed file
validPhe: Validate a phenotype file
write.phe.table: Write a phenotype data.frame to file

Functions

.FilePath Man page
.PlGwasC Man page
.PlInfoC Man page
.RbedInfoC Man page
.ReadInfo Man page
CollapsABEL Man page
CollapsABEL-package Man page
FilePath-class Man page
PlGwasC-class Man page
PlInfoC-class Man page
RbedInfoC-class Man page
ReadInfo-class Man page
\%||\% Man page
alphaNumeric Man page
appChr Source code
asBigMatrix Man page
asBigMatrix,data.frame,ANY,ANY,ANY,ANY,ANY,ANY,ANY,logical-metho Man page
asBigMatrix,matrix,ANY,ANY,ANY,ANY,ANY,ANY,ANY,logical-method Man page
asBigMatrix,vector,ANY,ANY,ANY,ANY,ANY,ANY,ANY,logical-method Man page
assocFilter Man page Source code
baseName Man page
baseName,FilePath-method Man page
bedSizeCorrect Man page Source code
bedcollr Man page Source code
bimCorrectTypes Man page Source code
bin2DescFilename Man page Source code
binPhe Man page Source code
bmAddCol Man page Source code
bmAttachBin Man page Source code
bmBinFilename Source code
bmConvertFun Man page Source code
bmCreate Source code
bmDescFilename Source code
bmFilename Man page Source code
bmFilepath Man page Source code
bytesSnp Man page Source code
chExt Man page Source code
chGwasTag Source code
changeByMap Man page Source code
charify Man page Source code
checkFileExist Man page Source code
cmh Man page Source code
colClasses Man page Source code
colCors Man page Source code
collClear Man page Source code
collapsabel Man page
collapsabel-package Man page
collapse Man page Source code
collapseMat Man page Source code
collenv Man page
connectSnpPair Man page Source code
contrastData Man page Source code
contrastPlot Man page Source code
correctDesc Man page Source code
correctTypes Man page Source code
correctTypes_methods Man page
covarNames Man page Source code
cytoband Man page Source code
datToVec Man page Source code
dbUpToDate Source code
desc2BinFilename Man page Source code
dir.create2 Man page Source code
dir2Tag Source code
dirName Man page
dirName,FilePath-method Man page
dummyPhe Source code
dummyTypeI Source code
eprint Man page Source code
evalFile Man page Source code
expand.grid.rev Source code
famCorrectTypes Man page Source code
fidIid Man page Source code
file.create2 Man page Source code
filePath Man page Source code
fileSize Man page Source code
frqUpToDate Source code
gcdhBmCreate Man page Source code
gcdhDir Man page Source code
gcdhPower Man page Source code
gcdhRegion Man page Source code
gcdhReport Man page Source code
getHaplo Man page Source code
getHaplos Man page Source code
getOrElse-operator Man page
getQuery Man page Source code
getr2 Man page Source code
glm2 Man page Source code
glmIter Man page Source code
gwasDat Man page Source code
gwasDir Man page Source code
gwasLog Man page Source code
gwasOut Man page Source code
gwasOutStem Man page Source code
gwasR Man page Source code
gwasRDS Man page Source code
haplo.g Source code
haploFormat Source code
haploString Source code
head2 Man page Source code
headPhe Man page Source code
infoFactory Source code
isBinary Man page Source code
isS4Class Man page Source code
isSQLite3 Man page Source code
isSetup Man page Source code
isSetupRbed Man page Source code
lagDistance Man page Source code
lenCheck Man page Source code
listEqual Man page Source code
listGwasTags Man page Source code
listTags Man page
loadGwas Man page Source code
mLogP Source code
makePhe Man page Source code
manhattanData Man page Source code
manhattanPlot Man page Source code
minimalPIndices Source code
nIndivApprPl Man page Source code
nIndivPl Man page Source code
nSnpPl Man page Source code
nonExistentFiles Man page Source code
numVectorSQLRepr Man page Source code
onLoad Source code
permutePhe Man page Source code
plGwas Man page
plGwas,PlGwasC,character,character,character,character,logical,l Man page
plGwas,RbedInfoC,character,character,character,character,logical Man page Man page
plGwas,RbedInfoC,character,character,character,character,missing Man page Man page
plGwas,RbedInfoC,character,character,missing,character,missing,m Man page
plInfo Man page
plInfo,PlInfoC,character,logical-method Man page
plInfo,PlInfoC,character,missing-method Man page
plInfo,missing,character,logical-method Man page
plInfo,missing,character,missing-method Man page
plTrim Man page Source code
plinkTrio Source code
plinkr Man page Source code
qq Man page Source code
qq2 Man page Source code
qqmulti Man page Source code
randNormDat Man page Source code
randomString Man page Source code
randomStrings Man page Source code
rbedInfo Man page Source code
read.phe.table Man page Source code
readAssoc Man page Source code
readBed Man page
readBed,RbedInfoC,ANY,logical,logical-method Man page
readBed,RbedInfoC,ANY,logical,missing-method Man page
readBed,RbedInfoC,ANY,missing,logical-method Man page
readBed,RbedInfoC,ANY,missing,missing-method Man page
readBed,RbedInfoC,missing,logical,logical-method Man page
readBed,RbedInfoC,missing,logical,missing-method Man page
readBed,RbedInfoC,missing,missing,logical-method Man page
readBed,RbedInfoC,missing,missing,missing-method Man page
readBim Man page
readBmBin Man page Source code
readDesc Man page Source code
readFactory Source code
readFam Man page
readFunFactory Man page Source code
readGwasOut Man page Source code
readInfo Man page
readInfo,character,character-method Man page
readInfo,character,missing-method Man page
readLiteral Man page Source code
readLogistic Man page Source code
readPhe Man page Source code
readPlinkOut Man page Source code
readQassoc Man page Source code
realBedSize Man page Source code
removeAllTags Source code
removeTag Man page Source code
reprClasses Man page Source code
rmFilesByStem Man page Source code
rmPlinkFiles Source code
runGcdh Man page Source code
runGwas Man page Source code
runTypeI Man page Source code
running.bool Source code
running.bools Source code
saveDesc Man page Source code
scaleByChr Source code
secondSnpIndices Source code
secondSnpIndices1 Source code
sendQuery Man page Source code
setOptModel Man page Source code
setup Man page Source code
setupRbed Man page Source code
shiftBed Man page Source code
shiftedStem Man page Source code
slurp Man page Source code
snpPos Man page Source code
snpRowId Man page Source code
spit Man page Source code
sqliteFileGcdh Source code
sqliteFilePl Man page Source code
stopFormat Man page Source code
strConcat Man page Source code
strVectorRepr Man page Source code
strVectorSQLRepr Man page Source code
systemFormat Man page Source code
tag2Dir Source code
tag2RDS Source code
tag2RDSPath Source code
tail2 Man page Source code
theoBedSize Man page Source code
type2Bytes Source code
validPhe Man page Source code
validatedIdx Source code
write.phe.table Man page Source code

Files

NAMESPACE
NEWS
R
R/0_strConcat.R
R/0_readFactory.R
R/1_bigmatrixUtils.R
R/3_permute.R
R/sysdata.rda
R/0_plinkr.R
R/1_rbedInfo.R
R/0_glm2.R
R/0_loadJava.R
R/0_lenCheck.R
R/0_nonExistentFiles.R
R/0_bedcollr.R
R/0_cytoband.R
R/1_bedinfo.R
R/0_sqlUtils.R
R/0__globalVars.R
R/0_filePath.R
R/snpPos.R
R/4_haplo.R
R/0_manhattan.R
R/0_head2.R
R/0_utils.R
R/2_plGwas.R
R/CollapsABEL.R
MD5
DESCRIPTION
man
man/stopFormat.Rd
man/manhattanData.Rd
man/shiftedStem.Rd
man/charify.Rd
man/fidIid.Rd
man/checkFileExist.Rd
man/gwasOutStem.Rd
man/chExt.Rd
man/getHaplos.Rd
man/nonExistentFiles.Rd
man/alphaNumeric.Rd
man/correctTypes_methods.Rd
man/strConcat.Rd
man/gcdhReport.Rd
man/runGcdh.Rd
man/plinkr.Rd
man/ReadInfo-class.Rd
man/isBinary.Rd
man/realBedSize.Rd
man/manhattanPlot.Rd
man/head2.Rd
man/plTrim.Rd
man/systemFormat.Rd
man/readBim.Rd
man/randomString.Rd
man/makePhe.Rd
man/asBigMatrix.Rd
man/gwasOut.Rd
man/readAssoc.Rd
man/colCors.Rd
man/readQassoc.Rd
man/readFam.Rd
man/changeByMap.Rd
man/getHaplo.Rd
man/numVectorSQLRepr.Rd
man/RbedInfoC-class.Rd
man/listGwasTags.Rd
man/plGwas.Rd
man/headPhe.Rd
man/snpRowId.Rd
man/nSnpPl.Rd
man/gwasDat.Rd
man/evalFile.Rd
man/filePath.Rd
man/readLiteral.Rd
man/isSQLite3.Rd
man/gwasLog.Rd
man/getQuery.Rd
man/plInfo.Rd
man/CollapsABEL.Rd
man/slurp.Rd
man/assocFilter.Rd
man/bedcollr.Rd
man/binPhe.Rd
man/colClasses.Rd
man/correctDesc.Rd
man/randNormDat.Rd
man/getOrElse-operator.Rd
man/rbedInfo.Rd
man/readLogistic.Rd
man/write.phe.table.Rd
man/loadGwas.Rd
man/file.create2.Rd
man/bimCorrectTypes.Rd
man/cytoband.Rd
man/bytesSnp.Rd
man/bmAddCol.Rd
man/readDesc.Rd
man/spit.Rd
man/gcdhBmCreate.Rd
man/desc2BinFilename.Rd
man/sendQuery.Rd
man/listEqual.Rd
man/readBed.Rd
man/snpPos.Rd
man/contrastData.Rd
man/nIndivPl.Rd
man/lenCheck.Rd
man/readBmBin.Rd
man/dirName.Rd
man/runTypeI.Rd
man/gwasR.Rd
man/connectSnpPair.Rd
man/validPhe.Rd
man/lagDistance.Rd
man/shiftBed.Rd
man/cmh.Rd
man/readInfo.Rd
man/gwasDir.Rd
man/randomStrings.Rd
man/gcdhPower.Rd
man/bmFilename.Rd
man/collClear.Rd
man/covarNames.Rd
man/dir.create2.Rd
man/datToVec.Rd
man/bmFilepath.Rd
man/bedSizeCorrect.Rd
man/readFunFactory.Rd
man/fileSize.Rd
man/removeTag.Rd
man/setupRbed.Rd
man/bmConvertFun.Rd
man/setOptModel.Rd
man/qq2.Rd
man/reprClasses.Rd
man/collapseMat.Rd
man/nIndivApprPl.Rd
man/baseName.Rd
man/isSetup.Rd
man/permutePhe.Rd
man/collenv.Rd
man/theoBedSize.Rd
man/gcdhDir.Rd
man/read.phe.table.Rd
man/bin2DescFilename.Rd
man/PlGwasC-class.Rd
man/gcdhRegion.Rd
man/isSetupRbed.Rd
man/readPhe.Rd
man/collapse.Rd
man/runGwas.Rd
man/eprint.Rd
man/qqmulti.Rd
man/FilePath-class.Rd
man/PlInfoC-class.Rd
man/readGwasOut.Rd
man/getr2.Rd
man/saveDesc.Rd
man/readPlinkOut.Rd
man/rmFilesByStem.Rd
man/famCorrectTypes.Rd
man/setup.Rd
man/strVectorSQLRepr.Rd
man/glmIter.Rd
man/qq.Rd
man/gwasRDS.Rd
man/strVectorRepr.Rd
man/sqliteFilePl.Rd
man/isS4Class.Rd
man/contrastPlot.Rd
man/bmAttachBin.Rd
man/glm2.Rd
CollapsABEL documentation built on May 19, 2017, 7:24 a.m.

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