gap-internalR Documentation

Internal functions for gap

Description

These are internal functions.

a2g gives allele-to-genotype conversion.

chr_pos_a1_a2 produces SNPID format.

g2a returns two alleles according to a genotype identifier.

g2a.c is the C version of g2c.

gc.control is used by gc.em().

gcode is as a2g.

grid2d is used to optional draw a 2-d grid according to chromosomal lengths.

grec2g is undocumented.

hap.control is used by hap.em().

HapDesign and HapFreqSE both accept a haplo.em object to derieve a design/dosage matrix and standard error of haplotype frequency estimates. The former is appropriate for haplotype trend regression (HTR), e.g., within the generalized linear model (GLM) framework to be equivllant to a formal approach as implemented in the package haplo.stats and hap.score. However, they are expected to be compatible with objects from gc.em() gc.em and hap.em. The two functions are included as courtesy of Prof Andrea Foulkes from the useR!2008 tutorial.

hap.score.glm, hap.score.podds are used by hap.score().

invlogit, inverse logit transformation.

inv_chr_pos_a1_a2 is the inverse function of chr_pos_a1_a2.

is.miss is undocumented.

KCC calculates disease prevalences in cases and controls for a given genotype relative risk, allele frequency and prevalencen of the disease in the whole population. It is used by tscc and pbsize2.

k obtains 1st and 2nd order culumants for correlation coefficient.

m2plem is an experimental function for PLEM format.

makeRLEplot for RLE plot.

sun3d is for 3D Manhattan plot according to Sun, et al. (2018).

micombine is used to combine imputation results.

plem2m is also experimental for PLEM format.

ReadGRM is a function to read GCTA grm.gz and grm.id file

ReadGRMPLINK is a function to read PLINK PI_HAT as a genomic relationship matrix.

ReadGRMPCA is a function to read .eigenval and .eigenvec files from gcta –pca.

ReadGRMBin is a function to read GCTA grm.bin files, modified from GCTA documentation.

revhap recovers the allele indices for a given haplotype ID in a multiallelic system.

revhap.i is similar to revhap.

solve.skol is a function used by tscc.

toETDT a function used to experiment with ETDT.

ungcode recovers alleles from genotype(s).

VR is a utility function for calculating variance of a ratio.

weighted.median is a function for obtaining weighted median with interpolation.

WriteGRM is a utility function to write GCTA grm.gz and grm.id files.

WriteGRMBin is a utility function to write GCTA grm.bin files.

WriteGRMSAS is a utility function to write a GRM object to SAS PROCs MIXED/GLIMMIX ldata.

x2 is a simple chi-squared test of two proportions.

z is a normal z-test of two proportions used by tscc.

Usage

a2g(a1,a2)
chr_pos_a1_a2(chr,pos,a1,a2,prefix="chr",seps=c(":","_","_"),uppercase=TRUE)
g2a(g)
g2a.c(g)
inv_chr_pos_a1_a2(chr_pos_a1_a2,prefix="chr",seps=c(":","_","_"))
KCC(model,GRR,p1,K)
sun3d(xyz="INF1.merge.cis.vs.trans",
      cols=c("id","chr1","pos1","chr2","pos2","gene","target","log10p","x","y","col"),
      xy.scale=c(1.3e8,1.3e8),marker.size=4,log10p.max=400,
      prefix=c("Sentinel","CHR","POS","CHR","POS","Gene","Target","-log10(p)"),
      postfix="\u003c/br>",
      json.file="d3.json",pretty=TRUE)
ReadGRM(prefix=51)
ReadGRMBin(prefix, AllN=FALSE, size=4)
ReadGRMPLINK(prefix, diag=1)
ReadGRMPCA(prefix)
revhap(loci,hapid)
VR(v1,vv1,v2,vv2,c12)
WriteGRM(prefix=51,id,N,GRM)
WriteGRMBin(prefix, grm, N, id, size=4)
WriteGRMSAS(grmlist, outfile="gwas")

Arguments

a1

Allele 1

a2

Allele 2

g

A genotype identifier

model

One of "multiplicative", "additive", "recessive", "dominant", "overdominant"

GRR

Genotype relative risk

p1

Frequency of the risk allele

K

Prevalence of disease in the population

loci

A vector of number of alleles at all loci

hapid

Haplotype identifier

Details

These functions are not so frequently called by users