CollapsABEL             CollapsABEL: an R library for detecting
                        compound heterozygote alleles in genome-wide
                        association or sequencing studies
FilePath-class          An S4 class to represent a file path
PlGwasC-class           An S4 class representing info about GWAS on
                        plink files
PlInfoC-class           An S4 class representing info about plink files
RbedInfoC-class         S4 class for necessary info to read a bed file
                        into R
ReadInfo-class          An S4 class to represent information about a
                        whitespace-delimited text file to be read into
                        R
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' run
baseName                Basename of a FilePath object
bedSizeCorrect          Check whether bed file is of correct size
bedcollr                Shift bed files
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 big.matrix
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.
chExt                   Change extension names
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
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
collClear               Clear up CollapsABEL workspace
collapse                Collpase genotypes
collapseMat             Collapse two genotype matrices, column by
                        column
collenv                 An environment for storing CollapsABEL package
                        local variables
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
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 with phenotypes
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 variables with fixed dependent
                        variables and covariates.
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
isSQLite3               Check whether a file is a SQLite3 database.
isSetup                 Check if a directory containing .bed .fam and
                        .bim files is properly setup
isSetupRbed             Check if an RbedInfoC object is properly set up
lagDistance             Distance with lag
lenCheck                Check each element of a list has expected
                        length Give a 'list(a, b, ...)' and 'vector(l1,
                        l2, ...)', check that length of a is equal to
                        l1, length of b is equal to l2, etc.
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
nSnpPl                  Get number of SNPs.
nonExistentFiles        Non-existent files from a vector of filenames
numVectorSQLRepr        String representation of a numeric vector for
                        SQLite consumption
permutePhe              Permute a phenotype file
plGwas                  Constructor for PlGwasC class
plInfo                  Constructor for PlInfoC class
plTrim                  Trim plink files
plinkr                  A wrapper for plink
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
read.phe.table          Read phenotype file
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 a data.frame, otherwise
                        returns NULL.
readInfo                ReadInfo constructor
readLiteral             Read a file literally (all columns as
                        character)
readLogistic            Read PLINK logistic regression output files.
readPhe                 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 consumption
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
