Man pages for CollapsABEL
Generalized CDH (GCDH) Analysis
| 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 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 |
