Description Usage Arguments Value Note Author(s) Examples
These function calculates summary statistics of each row or column of
call rates and heterozygosity for each row of a an
object of class "SnpMatrix"
or "XSnpMatrix"
1 2 | row.summary(object)
col.summary(object, rules = NULL, uncertain = TRUE)
|
object |
genotype data as a |
rules |
An object of class
|
uncertain |
If |
row.summary |
returns a data frame with rows corresponding to rows of the input object and with columns/elements:
Uncertain calls are ignored for calculating the heterozygosity. |
col.summary |
returns a data frame with rows corresponding to columns of the input object and with columns/elements:
For objects of class
|
The current version of row.summary
does not deal with the X chromosome
differently, so that males are counted as homozygous.
David Clayton dc208@cam.ac.uk
1 2 3 4 5 6 7 | data(testdata)
rs <- row.summary(Autosomes)
summary(rs)
cs <- col.summary(Autosomes)
summary(cs)
cs <- col.summary(Xchromosome)
summary(cs)
|
Loading required package: survival
Loading required package: Matrix
Call.rate Certain.calls Heterozygosity
Min. :0.6577 Min. :1 Min. :0.2182
1st Qu.:0.6963 1st Qu.:1 1st Qu.:0.2550
Median :0.9455 Median :1 Median :0.2599
Mean :0.8657 Mean :1 Mean :0.2598
3rd Qu.:0.9628 3rd Qu.:1 3rd Qu.:0.2642
Max. :0.9781 Max. :1 Max. :0.2820
Calls Call.rate Certain.calls RAF
Min. : 0.0 Min. :0.0000 Min. :1 Min. :0.0000
1st Qu.:265.0 1st Qu.:0.6625 1st Qu.:1 1st Qu.:0.1610
Median :394.0 Median :0.9850 Median :1 Median :0.4775
Mean :346.3 Mean :0.8657 Mean :1 Mean :0.4882
3rd Qu.:398.0 3rd Qu.:0.9950 3rd Qu.:1 3rd Qu.:0.8166
Max. :400.0 Max. :1.0000 Max. :1 Max. :1.0000
NA's :43 NA's :43
MAF P.AA P.AB P.BB
Min. :0.0000 Min. :0.00000 Min. :0.00000 Min. :0.00000
1st Qu.:0.0325 1st Qu.:0.03275 1st Qu.:0.06172 1st Qu.:0.02506
Median :0.1713 Median :0.26984 Median :0.28444 Median :0.22822
Mean :0.1920 Mean :0.38189 Mean :0.25975 Mean :0.35836
3rd Qu.:0.3289 3rd Qu.:0.70551 3rd Qu.:0.43609 3rd Qu.:0.66582
Max. :0.5000 Max. :1.00000 Max. :1.00000 Max. :1.00000
NA's :43 NA's :43 NA's :43 NA's :43
z.HWE
Min. :-19.9499
1st Qu.: -0.5980
Median : 0.0754
Mean : -0.0197
3rd Qu.: 0.6803
Max. : 16.2481
NA's :1254
Calls Call.rate Certain.calls RAF
Min. : 0.0 Min. :0.0000 Min. :1 Min. :0.00000
1st Qu.:264.0 1st Qu.:0.6600 1st Qu.:1 1st Qu.:0.08831
Median :389.0 Median :0.9725 Median :1 Median :0.45126
Mean :333.8 Mean :0.8345 Mean :1 Mean :0.46021
3rd Qu.:397.0 3rd Qu.:0.9925 3rd Qu.:1 3rd Qu.:0.83244
Max. :400.0 Max. :1.0000 Max. :1 Max. :1.00000
NA's :2 NA's :2
MAF P.AA P.AB P.BB
Min. :0.000000 Min. :0.00000 Min. :0.00000 Min. :0.000000
1st Qu.:0.007812 1st Qu.:0.03226 1st Qu.:0.01081 1st Qu.:0.005405
Median :0.113990 Median :0.30811 Median :0.18852 Median :0.195652
Mean :0.174095 Mean :0.42316 Mean :0.23098 Mean :0.345855
3rd Qu.:0.313218 3rd Qu.:0.83607 3rd Qu.:0.43784 3rd Qu.:0.655462
Max. :0.496552 Max. :1.00000 Max. :0.72283 Max. :1.000000
NA's :2 NA's :2 NA's :2 NA's :2
P.A P.B z.HWE Calls.diploid
Min. :0.0000 Min. :0.00000 Min. :-3.60226 Min. : 0.0
1st Qu.:0.1619 1st Qu.:0.07729 1st Qu.:-0.55347 1st Qu.:122.0
Median :0.5461 Median :0.45390 Median : 0.13749 Median :184.0
Mean :0.5430 Mean :0.45699 Mean : 0.06628 Mean :157.5
3rd Qu.:0.9227 3rd Qu.:0.83810 3rd Qu.: 0.51360 3rd Qu.:186.0
Max. :1.0000 Max. :1.00000 Max. : 7.67702 Max. :186.0
NA's :2 NA's :2 NA's :36
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