locus: Create and Manipulate Locus, Gene, and Marker Objects
In genetics: Population Genetics
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
locus, gene, and marker create objects to store
information, respectively, about genetic loci, genes, and markers.
is.locus, is.gene, and ismarker test whether an
object is a member of the respective class.
as.character.locus, as.character.gene,
as.character.marker return a character string containing a
compact encoding the object.
getlocus, getgene, getmarker extract locus data
(if present) from another object.
locus<-, marker<-, and gene<- adds locus data to
an object.
Usage
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locus(name, chromosome, arm=c("p", "q", "long", "short", NA),
index.start, index.end=NULL)
gene(name, chromosome, arm=c("p", "q", "long", "short"),
index.start, index.end=NULL)
marker(name, type, locus.name, bp.start, bp.end = NULL,
relative.to = NULL, ...)
is.locus(x)
is.gene(x)
is.marker(x)
## S3 method for class 'locus'
as.character(x, ...)
## S3 method for class 'gene'
as.character(x, ...)
## S3 method for class 'marker'
as.character(x, ...)
getlocus(x, ...)
locus(x) <- value
marker(x) <- value
gene(x) <- value
Arguments
name
character string giving locus, gene, or marker name
chromosome
integer specifying chromosome number (1:23 for humans).
arm
character indicating long or short arm of the chromosome.
Long is be specified by "long" or "p". Short is specified by
"short" or "q".
index.start
integer specifying location of start of locus or
gene on the chromosome.
index.end
optional integer specifying location of end of locus or
gene on the chromosome.
type
character string indicating marker type, e.g. "SNP"
locus.name
either a character string giving the name of the
locus or gene (other details may be specified using ...) or a
locus or gene object.
bp.start
start location of marker, in base pairs
bp.end
end location of marker, in base pairs (optional)
relative.to
location (optional) from which bp.start and
bp.end are calculated.
...
parameters for locus used to fill in additional
details on the locus or gene within which the marker is located.
x
an object of class locus, gene, or
marker, or (for getlocus, locus<-,
marker<-, and gene<-) an object that may contain a locus
attribute or field, notably a genotype object.
value
locus, marker, or gene object
Value
Object of class locus and geneare lists with the
elements:
name
character string giving locus, gene, or marker name
chromosome
integer specifying chromosome number (1:23 for humans).
arm
character indicating long or short arm of the chromosome.
Long is be specified by "long" or "p". Short is specified by
"short" or "q".
index.start
integer specifying location of start of locus or
gene on the chromosome.
index.end
optional integer specifying location of end of locus or
gene on the chromosome.
Objects of class marker add the additional fields:
marker.name
character string giving the name of the marker
bp.start
start location of marker, in base pairs
bp.end
end location of marker, in base pairs (optional)
relative.to
location (optional) from which bp.start and
bp.end are calculated.
Author(s)
Gregory R. Warnes greg@warnes.net
See Also
Examples
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ar2 <- gene("AR2",chromosome=7,arm="q",index.start=35)
ar2
par <- locus(name="AR2 Psedogene",
chromosome=1,
arm="q",
index.start=32,
index.end=42)
par
c109t <- marker(name="C-109T",
type="SNP",
locus.name="AR2",
chromosome=7,
arm="q",
index.start=35,
bp.start=-109,
relative.to="start of coding region")
c109t
c109t <- marker(name="C-109T",
type="SNP",
locus=ar2,
bp.start=-109,
relative.to="start of coding region")
c109t
example.data <- c("D/D","D/I","D/D","I/I","D/D",
"D/D","D/D","D/D","I/I","")
g1 <- genotype(example.data, locus=ar2)
g1
getlocus(g1)
summary(g1)
HWE.test(g1)
g2 <- genotype(example.data, locus=c109t)
summary(g2)
getlocus(g2)
heterozygote(g2)
homozygote(g1)
allele(g1,1)
carrier(g1,"I")
heterozygote(g2)
Example output
Loading required package: combinat
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata:
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata:
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
Attaching package: 'genetics'
The following objects are masked from 'package:base':
%in%, as.factor, order
Gene: AR2 (7q35)
Locus: AR2 Psedogene (1q32-42)
Marker: AR2:C-109T (7q35:-109) Type: SNP
Marker: AR2:C-109T (7q35:-109) Type: SNP
Gene: AR2 (7q35)
[1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" NA
Alleles: D I
Gene: AR2 (7q35)
[1] NA
Alleles: D I
Gene: AR2 (7q35)
Number of samples typed: 9 (90%)
Allele Frequency: (2 alleles)
Count Proportion
D 13 0.72
I 5 0.28
NA 2 NA
Genotype Frequency:
Count Proportion
D/D 6 0.67
D/I 1 0.11
I/I 2 0.22
NA 1 NA
Heterozygosity (Hu) = 0.4248366
Poly. Inf. Content = 0.32074
-----------------------------------
Test for Hardy-Weinberg-Equilibrium
-----------------------------------
Call:
HWE.test.genotype(x = g1)
Raw Disequlibrium for each allele pair (D)
D I
D -0.1450617
I -0.1450617
Scaled Disequlibrium for each allele pair (D')
D I
D -1.88
I -1.88
Correlation coefficient for each allele pair (r)
D I
D 0.7230769
I 0.7230769
Observed vs Expected Allele Frequencies
Obs Exp Obs-Exp
D/D 0.66666667 0.52160494 0.1450617
I/D 0.05555556 0.20061728 -0.1450617
D/I 0.05555556 0.20061728 -0.1450617
I/I 0.22222222 0.07716049 0.1450617
Overall Values
Value
D -0.1450617
D' -1.8800000
r 0.7230769
Confidence intervals computed via bootstrap using 1000 samples
* WARNING: The R^2 disequlibrium statistics is bounded between
* [0,1]. The confidence intervals for R^2 values near 0 and 1 are
* ill-behaved. A rough correction has been applied, but the
* intervals still may not be correct for R^2 values near 0 or 1.
Observed 95% CI NA's Contains Zero?
Overall D -0.145061728 (-0.246913580, 0.012345679) 0 YES
Overall D' -1.880000000 (-8.000000000, 0.125000000) 24 YES
Overall r 0.723076923 (-0.125000000, 1.000000000) 24 YES
Overall R^2 0.522840237 ( 0.003460208, 1.000000000) 24 *NO*
Significance Test:
Exact Test for Hardy-Weinberg Equilibrium
data: g1
N11 = 6, N12 = 1, N22 = 2, N1 = 13, N2 = 5, p-value = 0.05882
Warning message:
In diseq.ci(x, R = ci.B, conf = conf) : NAs returned from diseq call
Marker: AR2:C-109T (7q35:-109) Type: SNP
Number of samples typed: 9 (90%)
Allele Frequency: (2 alleles)
Count Proportion
D 13 0.72
I 5 0.28
NA 2 NA
Genotype Frequency:
Count Proportion
D/D 6 0.67
D/I 1 0.11
I/I 2 0.22
NA 1 NA
Heterozygosity (Hu) = 0.4248366
Poly. Inf. Content = 0.32074
Marker: AR2:C-109T (7q35:-109) Type: SNP
[1] NA
Alleles: D I
[1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE NA
attr(,"locus")
Marker: AR2:C-109T (7q35:-109) Type: SNP
[1] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NA
attr(,"locus")
Gene: AR2 (7q35)
[1] "D" "D" "D" "I" "D" "D" "D" "D" "I" NA
attr(,"locus")
Gene: AR2 (7q35)
attr(,"which")
[1] 1
attr(,"allele.names")
[1] "D" "I"
[1] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE NA
attr(,"allele")
[1] NA
attr(,"locus")
Gene: AR2 (7q35)
[1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE NA
attr(,"locus")
Marker: AR2:C-109T (7q35:-109) Type: SNP
genetics documentation built on March 1, 2021, 9:06 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) See Also Examples
Description
locus, gene, and marker create objects to store
information, respectively, about genetic loci, genes, and markers.
is.locus, is.gene, and ismarker test whether an
object is a member of the respective class.
as.character.locus, as.character.gene,
as.character.marker return a character string containing a
compact encoding the object.
getlocus, getgene, getmarker extract locus data
(if present) from another object.
locus<-, marker<-, and gene<- adds locus data to
an object.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | locus(name, chromosome, arm=c("p", "q", "long", "short", NA),
index.start, index.end=NULL)
gene(name, chromosome, arm=c("p", "q", "long", "short"),
index.start, index.end=NULL)
marker(name, type, locus.name, bp.start, bp.end = NULL,
relative.to = NULL, ...)
is.locus(x)
is.gene(x)
is.marker(x)
## S3 method for class 'locus'
as.character(x, ...)
## S3 method for class 'gene'
as.character(x, ...)
## S3 method for class 'marker'
as.character(x, ...)
getlocus(x, ...)
locus(x) <- value
marker(x) <- value
gene(x) <- value
|
Arguments
name |
character string giving locus, gene, or marker name |
chromosome |
integer specifying chromosome number (1:23 for humans). |
arm |
character indicating long or short arm of the chromosome. Long is be specified by "long" or "p". Short is specified by "short" or "q". |
index.start |
integer specifying location of start of locus or gene on the chromosome. |
index.end |
optional integer specifying location of end of locus or gene on the chromosome. |
type |
character string indicating marker type, e.g. "SNP" |
locus.name |
either a character string giving the name of the
locus or gene (other details may be specified using |
bp.start |
start location of marker, in base pairs |
bp.end |
end location of marker, in base pairs (optional) |
relative.to |
location (optional) from which |
... |
parameters for |
x |
an object of class |
value |
|
Value
Object of class locus and geneare lists with the
elements:
name |
character string giving locus, gene, or marker name |
chromosome |
integer specifying chromosome number (1:23 for humans). |
arm |
character indicating long or short arm of the chromosome. Long is be specified by "long" or "p". Short is specified by "short" or "q". |
index.start |
integer specifying location of start of locus or gene on the chromosome. |
index.end |
optional integer specifying location of end of locus or gene on the chromosome. |
Objects of class marker add the additional fields:
marker.name |
character string giving the name of the marker |
bp.start |
start location of marker, in base pairs |
bp.end |
end location of marker, in base pairs (optional) |
relative.to |
location (optional) from which |
Author(s)
Gregory R. Warnes greg@warnes.net
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 | ar2 <- gene("AR2",chromosome=7,arm="q",index.start=35)
ar2
par <- locus(name="AR2 Psedogene",
chromosome=1,
arm="q",
index.start=32,
index.end=42)
par
c109t <- marker(name="C-109T",
type="SNP",
locus.name="AR2",
chromosome=7,
arm="q",
index.start=35,
bp.start=-109,
relative.to="start of coding region")
c109t
c109t <- marker(name="C-109T",
type="SNP",
locus=ar2,
bp.start=-109,
relative.to="start of coding region")
c109t
example.data <- c("D/D","D/I","D/D","I/I","D/D",
"D/D","D/D","D/D","I/I","")
g1 <- genotype(example.data, locus=ar2)
g1
getlocus(g1)
summary(g1)
HWE.test(g1)
g2 <- genotype(example.data, locus=c109t)
summary(g2)
getlocus(g2)
heterozygote(g2)
homozygote(g1)
allele(g1,1)
carrier(g1,"I")
heterozygote(g2)
|
Example output
Loading required package: combinat
Attaching package: 'combinat'
The following object is masked from 'package:utils':
combn
Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata:
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata:
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
Loading required package: MASS
Loading required package: mvtnorm
NOTE: THIS PACKAGE IS NOW OBSOLETE.
The R-Genetics project has developed an set of enhanced genetics
packages to replace 'genetics'. Please visit the project homepage
at http://rgenetics.org for informtion.
Attaching package: 'genetics'
The following objects are masked from 'package:base':
%in%, as.factor, order
Gene: AR2 (7q35)
Locus: AR2 Psedogene (1q32-42)
Marker: AR2:C-109T (7q35:-109) Type: SNP
Marker: AR2:C-109T (7q35:-109) Type: SNP
Gene: AR2 (7q35)
[1] "D/D" "D/I" "D/D" "I/I" "D/D" "D/D" "D/D" "D/D" "I/I" NA
Alleles: D I
Gene: AR2 (7q35)
[1] NA
Alleles: D I
Gene: AR2 (7q35)
Number of samples typed: 9 (90%)
Allele Frequency: (2 alleles)
Count Proportion
D 13 0.72
I 5 0.28
NA 2 NA
Genotype Frequency:
Count Proportion
D/D 6 0.67
D/I 1 0.11
I/I 2 0.22
NA 1 NA
Heterozygosity (Hu) = 0.4248366
Poly. Inf. Content = 0.32074
-----------------------------------
Test for Hardy-Weinberg-Equilibrium
-----------------------------------
Call:
HWE.test.genotype(x = g1)
Raw Disequlibrium for each allele pair (D)
D I
D -0.1450617
I -0.1450617
Scaled Disequlibrium for each allele pair (D')
D I
D -1.88
I -1.88
Correlation coefficient for each allele pair (r)
D I
D 0.7230769
I 0.7230769
Observed vs Expected Allele Frequencies
Obs Exp Obs-Exp
D/D 0.66666667 0.52160494 0.1450617
I/D 0.05555556 0.20061728 -0.1450617
D/I 0.05555556 0.20061728 -0.1450617
I/I 0.22222222 0.07716049 0.1450617
Overall Values
Value
D -0.1450617
D' -1.8800000
r 0.7230769
Confidence intervals computed via bootstrap using 1000 samples
* WARNING: The R^2 disequlibrium statistics is bounded between
* [0,1]. The confidence intervals for R^2 values near 0 and 1 are
* ill-behaved. A rough correction has been applied, but the
* intervals still may not be correct for R^2 values near 0 or 1.
Observed 95% CI NA's Contains Zero?
Overall D -0.145061728 (-0.246913580, 0.012345679) 0 YES
Overall D' -1.880000000 (-8.000000000, 0.125000000) 24 YES
Overall r 0.723076923 (-0.125000000, 1.000000000) 24 YES
Overall R^2 0.522840237 ( 0.003460208, 1.000000000) 24 *NO*
Significance Test:
Exact Test for Hardy-Weinberg Equilibrium
data: g1
N11 = 6, N12 = 1, N22 = 2, N1 = 13, N2 = 5, p-value = 0.05882
Warning message:
In diseq.ci(x, R = ci.B, conf = conf) : NAs returned from diseq call
Marker: AR2:C-109T (7q35:-109) Type: SNP
Number of samples typed: 9 (90%)
Allele Frequency: (2 alleles)
Count Proportion
D 13 0.72
I 5 0.28
NA 2 NA
Genotype Frequency:
Count Proportion
D/D 6 0.67
D/I 1 0.11
I/I 2 0.22
NA 1 NA
Heterozygosity (Hu) = 0.4248366
Poly. Inf. Content = 0.32074
Marker: AR2:C-109T (7q35:-109) Type: SNP
[1] NA
Alleles: D I
[1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE NA
attr(,"locus")
Marker: AR2:C-109T (7q35:-109) Type: SNP
[1] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE NA
attr(,"locus")
Gene: AR2 (7q35)
[1] "D" "D" "D" "I" "D" "D" "D" "D" "I" NA
attr(,"locus")
Gene: AR2 (7q35)
attr(,"which")
[1] 1
attr(,"allele.names")
[1] "D" "I"
[1] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE TRUE NA
attr(,"allele")
[1] NA
attr(,"locus")
Gene: AR2 (7q35)
[1] FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE NA
attr(,"locus")
Marker: AR2:C-109T (7q35:-109) Type: SNP
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