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CollapsABEL (version 0.10.11)

Generalized CDH (GCDH) Analysis

Description

Implements a generalized version of the CDH test ( and ) 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.

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Version

Install

install.packages('CollapsABEL')

Monthly Downloads

21

Version

0.10.11

License

GPL-3

Maintainer

Kaiyin Zhong

Last Published

December 11th, 2016

Functions in CollapsABEL (0.10.11)

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

bin2DescFilename

Convert a .bin filename to a .desc filename

bimCorrectTypes

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

correctTypes_methods

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

desc2BinFilename

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.

numVectorSQLRepr

String representation of a numeric vector for SQLite consumption

List GWAS or GCDH tags

Load PlGwasC object by tag, from the RDS file

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

famCorrectTypes

Correct types of fam data.frame

Estimate percentage of variation explained

GLM with arbitrary column names

Head and tail in two dimensions

getOrElse-operator

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

nonExistentFiles

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 simulations to control type-I error

Stop with format string

SQLite file of a PlInfoC object

strVectorSQLRepr

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.phe.table

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