summary.check.marker: Summary of check.marker object

In GenABEL: genome-wide SNP association analysis

Description

Provides cross-tabulation summarising number of marker which did not pass this or that criteria

Usage

	## S3 method for class 'check.marker'
summary(object, ...)

Arguments

object	object of class check.marker-class
...	additional arguments (not used)

Value

A list containing 2 tables: per-marker and per-person inconsistencies

Author(s)

Yurii Aulchenko

See Also

check.marker, check.marker-class

Examples

require(GenABEL.data)
data(srdta)
mc <- check.marker(srdta,ids=c(1:500))
summary(mc)

Example output

Loading required package: MASS
Loading required package: GenABEL.data
Excluding people/markers with extremely low call rate...
833 markers and 500 people in total
0 people excluded because of call rate < 0.1 
0 markers excluded because of call rate < 0.1 
Passed: 833 markers and 500 people

RUN 1 
833 markers and 500 people in total
11 (1.320528%) markers excluded as having low (<0.5%) minor allele frequency
355 (42.61705%) markers excluded because of low (<95%) call rate
2 (0.240096%) markers excluded because they are out of HWE (FDR <0.2)
122 (24.4%) people excluded because of low (<95%) call rate
Mean autosomal HET is 0.3309112 (s.e. 0.04850843)
0 people excluded because too high autosomal heterozygosity (FDR <1%)
Mean IBS is 0.7352585 (s.e. 0.02960414), as based on 472 autosomal markers
10 (2%) people excluded because of too high IBS (>=0.95)
In total, 472 (56.66267%) markers passed all criteria
In total, 371 (74.2%) people passed all criteria

RUN 2 
472 markers and 371 people in total
1 (0.2118644%) markers excluded as having low (<0.6738544%) minor allele frequency
41 (8.686441%) markers excluded because of low (<95%) call rate
0 (0%) markers excluded because they are out of HWE (FDR <0.2)
8 (2.156334%) people excluded because of low (<95%) call rate
Mean autosomal HET is 0.3301476 (s.e. 0.05067406)
0 people excluded because too high autosomal heterozygosity (FDR <1%)
Mean IBS is 0.7338261 (s.e. 0.03007232), as based on 430 autosomal markers
0 (0%) people excluded because of too high IBS (>=0.95)
In total, 430 (91.10169%) markers passed all criteria
In total, 363 (97.84367%) people passed all criteria

RUN 3 
430 markers and 363 people in total
0 (0%) markers excluded as having low (<0.6887052%) minor allele frequency
0 (0%) markers excluded because of low (<95%) call rate
0 (0%) markers excluded because they are out of HWE (FDR <0.2)
0 (0%) people excluded because of low (<95%) call rate
Mean autosomal HET is 0.3297729 (s.e. 0.05081398)
0 people excluded because too high autosomal heterozygosity (FDR <1%)
Mean IBS is 0.7338523 (s.e. 0.03009551), as based on 430 autosomal markers
0 (0%) people excluded because of too high IBS (>=0.95)
In total, 430 (100%) markers passed all criteria
In total, 363 (100%) people passed all criteria
$`Per-SNP fails statistics`
          NoCall NoMAF NoHWE Redundant Xsnpfail
NoCall       389     7     0         0        0
NoMAF         NA     5     0         0        0
NoHWE         NA    NA     2         0        0
Redundant     NA    NA    NA         0        0
Xsnpfail      NA    NA    NA        NA        0

$`Per-person fails statistics`
            IDnoCall HetFail IBSFail isfemale ismale isXXY otherSexErr
IDnoCall         127       0       3        0      0     0           0
HetFail           NA       0       0        0      0     0           0
IBSFail           NA      NA       7        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

GenABEL documentation built on May 30, 2017, 3:36 a.m.