Class "check.marker"

Description

This class contains results of genotypic quality control. This is an list object, usually generated by check.marker.

Names

snpok

Markers which passed all criteria

idok

People which passed all criteria

nohwe

Markers which did not pass HWE check

Pex.nohwe

Exact HWE P-values for markers which did not pass HWE check

nocall

Markers with call rate < specified callrate

nofreq

Markers with MAF < specified maf

Xmrkfail

X-linked markers with too many heterozygous male genotypes

redundant

Redundant markers

details.redundancy

List with details on redundant markers (reference-marker <-> redundant-markers)

idnocall

People with too low SNP call rate across al SNPs

hetfail

People having too high heterozygosity

ibsfail

People having too high IBS with other people

Xidfail

Men with too many heterozygous X-linked markers

call

List with details on call: call, name (of marker), map, chromosome

Methods

summary

signature(object = "check.marker"): gives a cross table summrising how many markers did not pass because of this or that criteria

plot

signature(object = "check.marker"): Plots summary of genotypic data QC

Author(s)

Yurii Aulchenko

See Also

check.marker, summary.check.marker, redundant, plot.check.marker

Examples

require(GenABEL.data)
data(srdta)
mc <- check.marker(data=srdta@gtdata[,1:100],redundant="all",maf=0.01,
					minconcordance=0.9,fdr=.1,ibs.mrk=0)
class(mc)
names(mc)
names(mc$call)
mc$nohwe
mc$Pex.nohwe
summary(mc)
plot(mc)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GenABEL)
Loading required package: MASS
Loading required package: GenABEL.data
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenABEL/check.marker-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: check.marker-class
> ### Title: Class "check.marker"
> ### Aliases: check.marker-class 'summary, check.marker-method' 'plot,
> ###   check.marker-method'
> ### Keywords: classes
> 
> ### ** Examples
> 
> require(GenABEL.data)
> data(srdta)
> mc <- check.marker(data=srdta@gtdata[,1:100],redundant="all",maf=0.01,
+ 					minconcordance=0.9,fdr=.1,ibs.mrk=0)
Excluding people/markers with extremely low call rate...
100 markers and 2500 people in total
0 people excluded because of call rate < 0.1 
0 markers excluded because of call rate < 0.1 
Passed: 100 markers and 2500 people

RUN 1 
100 markers and 2500 people in total
0 (0%) markers excluded as having low (<1%) minor allele frequency
37 (37%) markers excluded because of low (<95%) call rate
2 (2%) markers excluded because they are out of HWE (FDR <0.1)
823 (32.92%) people excluded because of low (<95%) call rate
Mean autosomal HET is 0.3487854 (s.e. 0.1133168)
0 people excluded because too high autosomal heterozygosity (FDR <1%)
In total, 61 (61%) markers passed all criteria
In total, 1677 (67.08%) people passed all criteria

RUN 2 
61 markers and 1677 people in total
0 (0%) markers excluded as having low (<1%) minor allele frequency
0 (0%) markers excluded because of low (<95%) call rate
0 (0%) markers excluded because they are out of HWE (FDR <0.1)
0 (0%) people excluded because of low (<95%) call rate
Mean autosomal HET is 0.3492996 (s.e. 0.1143979)
0 people excluded because too high autosomal heterozygosity (FDR <1%)
In total, 61 (100%) markers passed all criteria
In total, 1677 (100%) people passed all criteria

CHECK REDUNDANCY
61 markers and 1677 people in total
6 (9.836066%) markers excluded as redundant (option = "all")
0 (0%) markers excluded as having low (<1%) minor allele frequency
0 (0%) markers excluded because of low (<95%) call rate
0 (0%) markers excluded because they are out of HWE (FDR <0.1)
418 (24.92546%) people excluded because of low (<95%) call rate
Mean autosomal HET is 0.3445665 (s.e. 0.1100367)
0 people excluded because too high autosomal heterozygosity (FDR <1%)
In total, 55 (90.16393%) markers passed all criteria
In total, 1259 (75.07454%) people passed all criteria
> class(mc)
[1] "check.marker"
> names(mc)
[1] "nofreq"             "nocall"             "nohwe"             
[4] "details.redundancy" "redundant"          "idnocall"          
[7] "snpok"              "idok"               "call"              
> names(mc$call)
[1] "name"       "ids"        "map"        "chromosome" "call"      
> mc$nohwe
[1] "rs73"  "rs128"
> mc$Pex.nohwe
NULL
> summary(mc)
$`Per-SNP fails statistics`
          NoCall NoMAF NoHWE Redundant Xsnpfail
NoCall        37     0     0         0        0
NoMAF         NA     0     0         0        0
NoHWE         NA    NA     2         0        0
Redundant     NA    NA    NA         6        0
Xsnpfail      NA    NA    NA        NA        0

$`Per-person fails statistics`
            IDnoCall HetFail IBSFail isfemale ismale isXXY otherSexErr
IDnoCall        1241       0       0        0      0     0           0
HetFail           NA       0       0        0      0     0           0
IBSFail           NA      NA       0        0      0     0           0
isfemale          NA      NA      NA        0      0     0           0
ismale            NA      NA      NA       NA      0     0           0
isXXY             NA      NA      NA       NA     NA     0           0
otherSexErr       NA      NA      NA       NA     NA    NA           0

> plot(mc)
Red: no call
Yellow: low frequency
Green: out of HWE
Cyan: redundant
Diagonal: redundant markers (reference presented as "+")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>