Shift bed files
Basename of a FilePath object
Filter a PlGwasC object by the results of a plink --assoc
run
Check whether bed file is of correct size
Convert a .bin filename to a .desc filename
Correct types of bim data.frame
Check whether phenotype of a GWAS is binary
Add column(s) to an existing big.matrix
Alpha-numeric characters
Coerce an R vector/matrix/data.frame into a big.matrix
Change extension names
Contrast Manhattan plot the simple way
Get number of bytes used by each SNP.
Transform a vector by a mapping
Convert certain columns of a data.frame to character type
Conversion function to use when appending values to a big.matrix
Attach a big.matrix by its bin filename
Stop when any file does not exist
Get classes of columns of a data.frame
Correlation coefficient of column-pairs of two data frames
Get covariate names of a GWAS
Create directory if it does not already exist
Directory name of a file path
An environment for storing CollapsABEL package local variables
Convert columns of a data frame to certain types
Correct description of big.matrix
Annotate a pair of SNPs in the contrast Manhattan plot
Find cytoband at a given position
Produce contrast Manhattan plot
Prepare data for contrastPlot
Extract one row or column of a data frame as a vector
Collapse two genotype matrices, column by column
Create a big.matrix under specified GCDH tag
Get file size
Convert a .desc filename to a .bin filename
Print quoted expression then its value
Eval R expressions from a file.
Clear up CollapsABEL workspace
GCDH power analysis
Create GCDH task directories by tag
Infer haplotypes for a pair of SNPs
GWAS output file name
Inferring haplotypes from two genotype data frames, and join with phenotypes
Generate a big.matrix filename (.bin or .desc)
Distance with lag
Check whether a file is a SQLite3 database.
Plink output filename
CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association or sequencing studies
Collpase genotypes
Get the big.matrix file path according to GCDH task tag
Check if a directory containing .bed .fam and .bim files is properly setup
Check if an RbedInfoC object is properly set up
Constructor for FilePath class
Create file if it does not already exist
Get number of SNPs.
String representation of a numeric vector for SQLite consumption
List GWAS or GCDH tags
Load PlGwasC object by tag, from the RDS file
Plink log fie
GWAS results directory of a certain GWAS scan
Check whether an S4 object is of a certain class
Constructor for PlGwasC class
Permute a phenotype file
Check whether a trait is binary
Read genotype and phenotype data into R
Perform glm iteratively through a number of independent variables with fixed dependent variables and covariates.
Run GCDH over a region
Generate a report from a GCDH run
Get RDS file path of a PlGwasC object
Invoke a GWAS in R
Trim plink files
Generate phenotype file from a fam file
QQ plot of one p-value vector
Prepare data for Manhattan plot.
Constructor for PlInfoC class
A wrapper for plink
FID and IID columns from fam file
Correct types of fam data.frame
Estimate percentage of variation explained
GLM with arbitrary column names
Head and tail in two dimensions
Default value for expression.
Get apparent number of individuals
Produce Manhattan plot
Read first n lines of a phenotype file
Check equality of two lists
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.
Get query results from a SQLite database
Get number of individuals
Non-existent files from a vector of filenames
Read genotypes from PLINK bed file into R
Read plink .bim files
Read columns into an R matrix from a big.matrix .bin file
Remove files by matching the starting part
Read big.matrix .desc file
Setup up a directory containing plink files
Set analysis model
Run GCDH analysis
QQ plot of multiple p-value vectors
QQ plot of two p-value vector
Read plink .fam files
Generate read_fun for ReadInfo class
Generate random strings
Constructor of RbedInfoC class
Run a GWAS
Run simulations to control type-I error
Stop with format string
SQLite file of a PlInfoC object
String representation of a character vector for SQLite consumption
Call system command with format string
Read phenotype file
Read plink output files
Add a "shift" suffix to a stem
Setup an RbedInfoC object
Theoretical size of bed file
Validate a phenotype file
Read a file literally (all columns as character)
Read PLINK .assoc files
Read phenotype file
Read .qassoc files
Read PLINK logistic regression output files.
File size of bed file
Save big.matrix description object to disk
Send query to SQLite database
Write a phenotype data.frame to file
Read a text file into a single string
Retrive SNP positions from UCSU database
Generate a m by n data.frame from normal distribution
Generate a single alpha-numeric random string
Read GWAS output from plink
If the GWAS is finished, returns a data.frame,
otherwise returns NULL.
ReadInfo constructor
Get row number of SNPs from their names
Represent classes of a data.frame in a character vector
Remove GWAS results by tag
Write strings to a file
String Representation of a character vector
Concatenate a vector of strings