CollapsABEL: Generalized CDH (GCDH) Analysis

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Implements a generalized version of the CDH test <DOI:10.1371/journal.pone.0028145> 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.

Author
Kaiyin Zhong, Fan Liu
Date of publication
2016-04-04 11:49:04
Maintainer
Kaiyin Zhong <kindlychung@gmail.com>
License
GPL-3
Version
0.10.8
URLs

View on CRAN

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
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
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
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
mh
Manhattan plot the simple way
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
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
snpPosSNP138
Retrive SNP positions from hg19 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

Files in this package

CollapsABEL
CollapsABEL/NAMESPACE
CollapsABEL/R
CollapsABEL/R/0_strConcat.R
CollapsABEL/R/0_readFactory.R
CollapsABEL/R/1_bigmatrixUtils.R
CollapsABEL/R/3_permute.R
CollapsABEL/R/0_globalVars.R
CollapsABEL/R/0_plinkr.R
CollapsABEL/R/1_rbedInfo.R
CollapsABEL/R/0_glm2.R
CollapsABEL/R/0_loadJava.R
CollapsABEL/R/0_lenCheck.R
CollapsABEL/R/0_nonExistentFiles.R
CollapsABEL/R/0_bedcollr.R
CollapsABEL/R/1_bedinfo.R
CollapsABEL/R/0_sqlUtils.R
CollapsABEL/R/0_filePath.R
CollapsABEL/R/0_manhattan.R
CollapsABEL/R/0_head2.R
CollapsABEL/R/0_utils.R
CollapsABEL/R/2_plGwas.R
CollapsABEL/R/CollapsABEL.R
CollapsABEL/MD5
CollapsABEL/DESCRIPTION
CollapsABEL/man
CollapsABEL/man/stopFormat.Rd
CollapsABEL/man/manhattanData.Rd
CollapsABEL/man/shiftedStem.Rd
CollapsABEL/man/charify.Rd
CollapsABEL/man/fidIid.Rd
CollapsABEL/man/checkFileExist.Rd
CollapsABEL/man/gwasOutStem.Rd
CollapsABEL/man/chExt.Rd
CollapsABEL/man/nonExistentFiles.Rd
CollapsABEL/man/alphaNumeric.Rd
CollapsABEL/man/correctTypes_methods.Rd
CollapsABEL/man/strConcat.Rd
CollapsABEL/man/gcdhReport.Rd
CollapsABEL/man/runGcdh.Rd
CollapsABEL/man/plinkr.Rd
CollapsABEL/man/mh.Rd
CollapsABEL/man/ReadInfo-class.Rd
CollapsABEL/man/isBinary.Rd
CollapsABEL/man/realBedSize.Rd
CollapsABEL/man/manhattanPlot.Rd
CollapsABEL/man/head2.Rd
CollapsABEL/man/plTrim.Rd
CollapsABEL/man/systemFormat.Rd
CollapsABEL/man/readBim.Rd
CollapsABEL/man/randomString.Rd
CollapsABEL/man/makePhe.Rd
CollapsABEL/man/asBigMatrix.Rd
CollapsABEL/man/gwasOut.Rd
CollapsABEL/man/readAssoc.Rd
CollapsABEL/man/colCors.Rd
CollapsABEL/man/readQassoc.Rd
CollapsABEL/man/readFam.Rd
CollapsABEL/man/changeByMap.Rd
CollapsABEL/man/numVectorSQLRepr.Rd
CollapsABEL/man/RbedInfoC-class.Rd
CollapsABEL/man/listGwasTags.Rd
CollapsABEL/man/plGwas.Rd
CollapsABEL/man/headPhe.Rd
CollapsABEL/man/snpRowId.Rd
CollapsABEL/man/nSnpPl.Rd
CollapsABEL/man/gwasDat.Rd
CollapsABEL/man/evalFile.Rd
CollapsABEL/man/filePath.Rd
CollapsABEL/man/readLiteral.Rd
CollapsABEL/man/isSQLite3.Rd
CollapsABEL/man/gwasLog.Rd
CollapsABEL/man/getQuery.Rd
CollapsABEL/man/plInfo.Rd
CollapsABEL/man/CollapsABEL.Rd
CollapsABEL/man/slurp.Rd
CollapsABEL/man/assocFilter.Rd
CollapsABEL/man/bedcollr.Rd
CollapsABEL/man/binPhe.Rd
CollapsABEL/man/colClasses.Rd
CollapsABEL/man/correctDesc.Rd
CollapsABEL/man/randNormDat.Rd
CollapsABEL/man/getOrElse-operator.Rd
CollapsABEL/man/rbedInfo.Rd
CollapsABEL/man/readLogistic.Rd
CollapsABEL/man/write.phe.table.Rd
CollapsABEL/man/snpPosSNP138.Rd
CollapsABEL/man/loadGwas.Rd
CollapsABEL/man/file.create2.Rd
CollapsABEL/man/bimCorrectTypes.Rd
CollapsABEL/man/bytesSnp.Rd
CollapsABEL/man/bmAddCol.Rd
CollapsABEL/man/readDesc.Rd
CollapsABEL/man/spit.Rd
CollapsABEL/man/gcdhBmCreate.Rd
CollapsABEL/man/desc2BinFilename.Rd
CollapsABEL/man/sendQuery.Rd
CollapsABEL/man/listEqual.Rd
CollapsABEL/man/readBed.Rd
CollapsABEL/man/contrastData.Rd
CollapsABEL/man/nIndivPl.Rd
CollapsABEL/man/lenCheck.Rd
CollapsABEL/man/readBmBin.Rd
CollapsABEL/man/dirName.Rd
CollapsABEL/man/runTypeI.Rd
CollapsABEL/man/gwasR.Rd
CollapsABEL/man/connectSnpPair.Rd
CollapsABEL/man/validPhe.Rd
CollapsABEL/man/lagDistance.Rd
CollapsABEL/man/shiftBed.Rd
CollapsABEL/man/readInfo.Rd
CollapsABEL/man/gwasDir.Rd
CollapsABEL/man/randomStrings.Rd
CollapsABEL/man/gcdhPower.Rd
CollapsABEL/man/bmFilename.Rd
CollapsABEL/man/collClear.Rd
CollapsABEL/man/covarNames.Rd
CollapsABEL/man/dir.create2.Rd
CollapsABEL/man/datToVec.Rd
CollapsABEL/man/bmFilepath.Rd
CollapsABEL/man/bedSizeCorrect.Rd
CollapsABEL/man/readFunFactory.Rd
CollapsABEL/man/fileSize.Rd
CollapsABEL/man/removeTag.Rd
CollapsABEL/man/setupRbed.Rd
CollapsABEL/man/bmConvertFun.Rd
CollapsABEL/man/setOptModel.Rd
CollapsABEL/man/reprClasses.Rd
CollapsABEL/man/collapseMat.Rd
CollapsABEL/man/nIndivApprPl.Rd
CollapsABEL/man/baseName.Rd
CollapsABEL/man/isSetup.Rd
CollapsABEL/man/permutePhe.Rd
CollapsABEL/man/collenv.Rd
CollapsABEL/man/theoBedSize.Rd
CollapsABEL/man/gcdhDir.Rd
CollapsABEL/man/read.phe.table.Rd
CollapsABEL/man/bin2DescFilename.Rd
CollapsABEL/man/PlGwasC-class.Rd
CollapsABEL/man/gcdhRegion.Rd
CollapsABEL/man/isSetupRbed.Rd
CollapsABEL/man/readPhe.Rd
CollapsABEL/man/collapse.Rd
CollapsABEL/man/runGwas.Rd
CollapsABEL/man/eprint.Rd
CollapsABEL/man/FilePath-class.Rd
CollapsABEL/man/PlInfoC-class.Rd
CollapsABEL/man/readGwasOut.Rd
CollapsABEL/man/getr2.Rd
CollapsABEL/man/saveDesc.Rd
CollapsABEL/man/readPlinkOut.Rd
CollapsABEL/man/rmFilesByStem.Rd
CollapsABEL/man/famCorrectTypes.Rd
CollapsABEL/man/setup.Rd
CollapsABEL/man/strVectorSQLRepr.Rd
CollapsABEL/man/glmIter.Rd
CollapsABEL/man/gwasRDS.Rd
CollapsABEL/man/strVectorRepr.Rd
CollapsABEL/man/sqliteFilePl.Rd
CollapsABEL/man/isS4Class.Rd
CollapsABEL/man/contrastPlot.Rd
CollapsABEL/man/bmAttachBin.Rd
CollapsABEL/man/glm2.Rd