trio.check: Check Case-Parent Trio Data for Mendelian Errors
In trio: Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
This function checks case-parent trio data in linkage or
genotype format for Mendelian errors. If no errors are found, the
function returns an object suitable for input to the trio.prepare
function. Otherwise, an object identifying the Mendelian errors is
returned.
Usage
1
trio.check(dat, is.linkage=TRUE, replace=FALSE)
Arguments
dat
A matrix or data frame of pedigree data in linkage format,
or in genotype format.
If the data are in linkage format, the file has to have the
standard linkage/pedigree format. Each row describes an individual,
and the columns are <famid> <pid> <fatid> <motid> <sex>
<affected> <genotype:1_1> <genotype:1_2> ... <genotype:n_1>
<genotype:n_2>. Here, <famid> is a unique identifier for
each family, <pid> is a unique identifier for an individual
within each family, <fatid> and <motid> identify the
father and mother of the individual, <sex> denotes the
gender, using the convention 1=male, 2=female, <affected>
denotes the disease status (0=unknown, 1=unaffected, 2=affected).
Only one phenotype column is allowed. Each genotype is encoded using
two columns (<genotype:k_1> and <genotype:k_2>),
identifying the alleles (1 for the major allele, 2 for the minor
allele, 0 if missing). Other values for the alleles will result in
an error. Please see the data frames trio.ped1 and
trio.ped2 contained in this package as examples for trio data
in linkage file format (complete and with missing records,
respectively).
If the data are in genotype format, each row in the
object describes an individual, and each block of three consecutive
rows describes the two parents and the affected child in a trio. The
columns in the object are <famid> <pid> <genotype_1>
... <genotype_n>. Here, <famid> is a unique identifier for
each family, <pid> is a unique identifier for an individual
within each family (with each block of three consecutive rows
describing the two parents and the affected child in a trio). Each
<genotype> is encoded as an integer indicating the number of
variant alleles (e.g. 0=common homozygote, 1=heterozygote, and
2=rare homozygote, and NA=missing genotype). Please see the
data frames trio.gen1 and trio.gen2 contained in this
package as examples for trio data in linkage file format (complete
and with missing records, respectively).
is.linkage
A logical value indicating if the case parent data
are in linkage file format (TRUE) or in genotype format
(FALSE).
replace
A logical value indicating whether existing Mendelian
errors should be replaced by missing values. For each Mendelian
error found (for a particular trio at a particular locus), all three
genotypes are replaced by NA, and an object suitable for
input to the trio.prepare function is returned.
Details
The first function used from this package should always be
trio.check. Unless otherwise specified, this function assumes
that the data are in linkage format, however, genotype data can also
be accommodated. If no Mendelian inconsistencies in the data provided
are identified, trio.check creates an object that can be
processed in the subsequent analysis with the trio.prepare
function. If the data were in linkage format, the genotype information
for each SNP will be converted into a single variable, denoting the
number of variant alleles.
To delineate the genotype information for the pseudo-controls in the
subsequent analysis, the trio data must not contain any Mendelian
errors. The function trio.check returns a warning, and an R
object with relevant information when Mendelian errors are encountered
in the supplied trio data. It is the users responsibility to find the
cause for the Mendelian errors and correct those, if
possible. However, Mendelian inconsistencies are often due to
genotyping errors and thus, it might not be possible to correct those
in a very straightforward manner. In this instance, the user might
want to encode the genotypes that cause theses Mendelian errors in
some of the trios as missing data. The function trio.check
allows for this possibility, using the argument replace=T.
Value
The function trio.check returns a list with the following
elements:
trio
A data frame with the genotypes of the trios, suitable for
input to the function trio.prepare. This element will be
NULL if Mendelian errors are detected.
errors
This element will be NULL if no Mendelian errors
are detected. Otherwise, this element will be a data frame with
five columns, indicating the Mendelian errors detected in the object
dat. The five columns of the data frame refer to the trio
(trio), the family id (famid), the genotype (snp), the row numbers (r),
and the column numbers (c).
trio.err
This element will be NULL if no Mendelian
errors are detected. Otherwise, this element will be a data frame
with the trio genotype data. If the input was a linkage file, the
data will be converted from alleles to genotypes. If the input was a
genotype file, this element will be identical to the input.
Author(s)
Qing Li, mail2qing@yahoo.com
References
Li, Q., Fallin, M.D., Louis, T.A., Lasseter, V.K., McGrath, J.A., Avramopoulos, D., Wolyniec, P.S., Valle, D., Liang, K.Y., Pulver, A.E.,
and Ruczinski, I. (2010). Detection of SNP-SNP Interactions in Trios of Parents with Schizophrenic Children. Genetic Epidemiology, 34, 396-406.
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
data(trio.data)
trio.tmp <- trio.check(dat=trio.ped1)
str(trio.tmp, max=1)
trio.tmp$trio[1:6,]
trio.tmp <- trio.check(dat=trio.ped.err)
str(trio.tmp, max=1)
trio.tmp$errors
trio.tmp$trio.err[1:3, c(1,2, 11:12)]
trio.ped.err[1:3,c(1:2, 23:26)]
trio.tmp <- trio.check(dat=trio.gen.err, is.linkage=FALSE)
trio.tmp$errors
trio.tmp$trio.err[1:6, c(1,2,7), drop=FALSE]
trio.rep <- trio.check(dat=trio.gen.err, is.linkage=FALSE, replace=TRUE)
trio.rep$trio[1:6,c(1,2,7)]
Example output
List of 2
$ trio :'data.frame': 300 obs. of 12 variables:
$ errors: NULL
famid pid snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10
1 10001 1 0 0 1 1 1 1 0 0 0 0
2 10001 2 0 2 0 0 2 0 0 0 0 0
3 10001 3 0 1 1 1 1 1 0 0 0 0
4 10002 1 0 0 2 2 0 2 0 0 0 1
5 10002 2 0 2 0 0 2 0 0 0 0 0
6 10002 3 0 1 1 1 1 1 0 0 0 0
[1] "Found Mendelian error(s)."
List of 3
$ trio : NULL
$ errors :'data.frame': 4 obs. of 5 variables:
$ trio.err:'data.frame': 300 obs. of 12 variables:
trio famid snp r c
1 1 10001 9 1 11
2 1 10001 10 1 12
3 2 10002 10 4 12
4 3 10003 10 7 12
famid pid snp9 snp10
1 10001 1 0 1
2 10001 2 0 2
3 10001 3 2 0
famid pid snp9_1 snp9_2 snp10_1 snp10_2
1 10001 1 1 1 1 2
2 10001 2 1 1 2 2
3 10001 3 2 2 1 1
[1] "Found Mendelian error(s)."
trio famid snp r c
1 1 2001 5 1 7
2 2 2002 5 4 7
famid pid snp5
6 2001 1 0
7 2001 2 0
5 2001 3 1
9 2002 1 1
10 2002 2 0
8 2002 3 2
famid pid snp5
6 2001 1 NA
7 2001 2 NA
5 2001 3 NA
9 2002 1 NA
10 2002 2 NA
8 2002 3 NA
trio documentation built on Nov. 8, 2020, 7:41 p.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
This function checks case-parent trio data in linkage or
genotype format for Mendelian errors. If no errors are found, the
function returns an object suitable for input to the trio.prepare
function. Otherwise, an object identifying the Mendelian errors is
returned.
Usage
1 | trio.check(dat, is.linkage=TRUE, replace=FALSE)
|
Arguments
dat |
A matrix or data frame of pedigree data in linkage format, or in genotype format. If the data are in linkage format, the file has to have the
standard linkage/pedigree format. Each row describes an individual,
and the columns are <famid> <pid> <fatid> <motid> <sex>
<affected> <genotype:1_1> <genotype:1_2> ... <genotype:n_1>
<genotype:n_2>. Here, <famid> is a unique identifier for
each family, <pid> is a unique identifier for an individual
within each family, <fatid> and <motid> identify the
father and mother of the individual, <sex> denotes the
gender, using the convention 1=male, 2=female, <affected>
denotes the disease status (0=unknown, 1=unaffected, 2=affected).
Only one phenotype column is allowed. Each genotype is encoded using
two columns (<genotype:k_1> and <genotype:k_2>),
identifying the alleles (1 for the major allele, 2 for the minor
allele, 0 if missing). Other values for the alleles will result in
an error. Please see the data frames If the data are in genotype format, each row in the
object describes an individual, and each block of three consecutive
rows describes the two parents and the affected child in a trio. The
columns in the object are <famid> <pid> <genotype_1>
... <genotype_n>. Here, <famid> is a unique identifier for
each family, <pid> is a unique identifier for an individual
within each family (with each block of three consecutive rows
describing the two parents and the affected child in a trio). Each
<genotype> is encoded as an integer indicating the number of
variant alleles (e.g. 0=common homozygote, 1=heterozygote, and
2=rare homozygote, and |
is.linkage |
A logical value indicating if the case parent data
are in linkage file format ( |
replace |
A logical value indicating whether existing Mendelian
errors should be replaced by missing values. For each Mendelian
error found (for a particular trio at a particular locus), all three
genotypes are replaced by |
Details
The first function used from this package should always be
trio.check. Unless otherwise specified, this function assumes
that the data are in linkage format, however, genotype data can also
be accommodated. If no Mendelian inconsistencies in the data provided
are identified, trio.check creates an object that can be
processed in the subsequent analysis with the trio.prepare
function. If the data were in linkage format, the genotype information
for each SNP will be converted into a single variable, denoting the
number of variant alleles.
To delineate the genotype information for the pseudo-controls in the
subsequent analysis, the trio data must not contain any Mendelian
errors. The function trio.check returns a warning, and an R
object with relevant information when Mendelian errors are encountered
in the supplied trio data. It is the users responsibility to find the
cause for the Mendelian errors and correct those, if
possible. However, Mendelian inconsistencies are often due to
genotyping errors and thus, it might not be possible to correct those
in a very straightforward manner. In this instance, the user might
want to encode the genotypes that cause theses Mendelian errors in
some of the trios as missing data. The function trio.check
allows for this possibility, using the argument replace=T.
Value
The function trio.check returns a list with the following
elements:
trio |
A data frame with the genotypes of the trios, suitable for
input to the function |
errors |
This element will be |
trio.err |
This element will be |
Author(s)
Qing Li, mail2qing@yahoo.com
References
Li, Q., Fallin, M.D., Louis, T.A., Lasseter, V.K., McGrath, J.A., Avramopoulos, D., Wolyniec, P.S., Valle, D., Liang, K.Y., Pulver, A.E., and Ruczinski, I. (2010). Detection of SNP-SNP Interactions in Trios of Parents with Schizophrenic Children. Genetic Epidemiology, 34, 396-406.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | data(trio.data)
trio.tmp <- trio.check(dat=trio.ped1)
str(trio.tmp, max=1)
trio.tmp$trio[1:6,]
trio.tmp <- trio.check(dat=trio.ped.err)
str(trio.tmp, max=1)
trio.tmp$errors
trio.tmp$trio.err[1:3, c(1,2, 11:12)]
trio.ped.err[1:3,c(1:2, 23:26)]
trio.tmp <- trio.check(dat=trio.gen.err, is.linkage=FALSE)
trio.tmp$errors
trio.tmp$trio.err[1:6, c(1,2,7), drop=FALSE]
trio.rep <- trio.check(dat=trio.gen.err, is.linkage=FALSE, replace=TRUE)
trio.rep$trio[1:6,c(1,2,7)]
|
Example output
List of 2
$ trio :'data.frame': 300 obs. of 12 variables:
$ errors: NULL
famid pid snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10
1 10001 1 0 0 1 1 1 1 0 0 0 0
2 10001 2 0 2 0 0 2 0 0 0 0 0
3 10001 3 0 1 1 1 1 1 0 0 0 0
4 10002 1 0 0 2 2 0 2 0 0 0 1
5 10002 2 0 2 0 0 2 0 0 0 0 0
6 10002 3 0 1 1 1 1 1 0 0 0 0
[1] "Found Mendelian error(s)."
List of 3
$ trio : NULL
$ errors :'data.frame': 4 obs. of 5 variables:
$ trio.err:'data.frame': 300 obs. of 12 variables:
trio famid snp r c
1 1 10001 9 1 11
2 1 10001 10 1 12
3 2 10002 10 4 12
4 3 10003 10 7 12
famid pid snp9 snp10
1 10001 1 0 1
2 10001 2 0 2
3 10001 3 2 0
famid pid snp9_1 snp9_2 snp10_1 snp10_2
1 10001 1 1 1 1 2
2 10001 2 1 1 2 2
3 10001 3 2 2 1 1
[1] "Found Mendelian error(s)."
trio famid snp r c
1 1 2001 5 1 7
2 2 2002 5 4 7
famid pid snp5
6 2001 1 0
7 2001 2 0
5 2001 3 1
9 2002 1 1
10 2002 2 0
8 2002 3 2
famid pid snp5
6 2001 1 NA
7 2001 2 NA
5 2001 3 NA
9 2002 1 NA
10 2002 2 NA
8 2002 3 NA
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