CollapsABEL v0.10.11

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Generalized CDH (GCDH) Analysis

Implements a generalized version of the CDH test (<DOI:10.1371/journal.pone.0028145> and <DOI:10.1186/s12859-016-1006-9>) 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.

Functions in CollapsABEL

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

Type Package
Date 2016-12-11
License GPL-3
URL https://bitbucket.org/kindlychung/collapsabel2/overview
BugReports https://bitbucket.org/kindlychung/collapsabel2/issues
SystemRequirements PLINK2, Java (>= 8.0), mysql
RoxygenNote 5.0.1
NeedsCompilation no
Packaged 2016-12-11 18:16:51 UTC; kaiyin
Repository CRAN
Date/Publication 2016-12-11 20:35:07

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