snp.subset: function to subset objects of class scan.gwaa and...
In GenABEL: genome-wide SNP association analysis

Description Usage Arguments Value Author(s) See Also Examples

Computing objects of class scan.gwaa may take long, especially when haplotypic analysis is performed. Therefore this function helps substracting results on some region (indicated by list of SNPs)

1	snp.subset(data, snpsubset)

`data`	object of class `scan.gwaa-class` or `check.marker-class`
`snpsubset`	character vector of snps to select

Object of class scan.gwaa-class or check.marker-class

Yurii Aulchenko

scan.gwaa-class, check.marker-class

require(GenABEL.data)
data(srdta)
# processing check.marker object
#mc <- check.marker(data=srdta@gtdata[,1:100],redundant="all",maf=0.01,
# minconcordance=0.9,fdr=.1,ibs.mrk=0)
mc <- check.marker(data=srdta@gtdata[,1:100],maf=0.01,fdr=.1,ibs.mrk=0)
summary(mc)
#plot(mc)
mc1 <- snp.subset(mc,snps=srdta@gtdata@snpnames[20:50])
summary(mc1)
#plot(mc1)
# processing scan.gwaa object
a <- qtscore(qt3~sex+age,data=srdta)
plot(a)
a1 <- snp.subset(a,snps=srdta@gtdata@snpnames[10:20])
plot(a1)

Loading required package: MASS
Loading required package: GenABEL.data
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
$`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         0        0
Xsnpfail      NA    NA    NA        NA        0

$`Per-person fails statistics`
            IDnoCall HetFail IBSFail isfemale ismale isXXY otherSexErr
IDnoCall         823       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

$`Per-SNP fails statistics`
          NoCall NoMAF NoHWE Redundant Xsnpfail
NoCall        11     0     0         0        0
NoMAF         NA     0     0         0        0
NoHWE         NA    NA     0         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           0       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

Warning messages:
1: In qtscore(qt3 ~ sex + age, data = srdta) :
  11 observations deleted due to missingness
2: In qtscore(qt3 ~ sex + age, data = srdta) :
  Lambda estimated < 1, set to 1