sw: Sliding Windows
In pegas: Population and Evolutionary Genetics Analysis System
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Applies a function over a matrix or a vector using sliding
windows. sw is a generic function with a method for
"DNAbin" matrices.
Usage
1
2
3
4
5
6
7
8
9
10
11
sw(x, width, step, ...)
## Default S3 method:
sw(x, width = 100, step = 50, POS = NULL,
FUN = mean, out.of.pos = NA_real_, na.rm = TRUE, L = NULL, ...)
## S3 method for class 'DNAbin'
sw(x, width = 100, step = 50, FUN = GC.content,
rowAverage = FALSE, quiet = TRUE, ...)
## S3 method for class 'sw'
plot(x, type = "l", xlab = "Position", x.scaling = 1,
show.ranges = FALSE, col.ranges = "blue",
lty.ranges = 1, lwd.ranges = 1, ...)
Arguments
x
a vector or a matrix.
width
an integer giving the window width.
step
an integer giving the step separating successive windows.
POS
a numeric vector giving the positions of the sites.
FUN
the function to be applied to the windows.
rowAverage
a logical value: if TRUE, FUN is
applied over all rows of x; if FALSE (the default)
FUN is applied to each row of x.
out.of.pos
the values used for the sites which are not in
POS.
na.rm
option passed to FUN.
L
the length of the chromosome (or sequence). If not given,
this is largest value in POS or the length of x if
POS is not given.
quiet
a logical value: if FALSE, the progress of the
calculations is printed.
type
the type of plotting (see plot.default).
xlab
the label under the x-axis.
x.scaling
the scaling of the x-axis.
show.ranges
a logical value specifying whether to show the
ranges of the windows with horizontal segments (ignored with a
warning if x is a matrix).
col.ranges, lty.ranges, lwd.ranges
arguments to modify the
appearance of the above segments (see segments).
...
further arguments passed to and from methods.
Details
FUN should return a single value.
x should be a matrix for the "DNAbin" method, or a
vector for the default one.
For the default method, the vector x is expanded into a vector
of length L (see above on how this value is found) and the
positions which are not in POS are filled with the value given
in out.of.pos. The resulting vector is then analysed with the
function FUN which must have an option na.rm. If the
function you want to use does not have this option, you can use
something like FUN = function(x, na.rm = TRUE)
foo(x[!is.na(x)]), replacing ‘foo’ by the name of your function. You
may also include more control on the handling of missing data.
Value
a matrix or a vector (if rowAverage = TRUE).
Author(s)
Emmanuel Paradis
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
data(woodmouse)
sw(woodmouse)
sw(woodmouse, 200, 200)
sw(woodmouse, 200, 200, rowAverage = TRUE)
## to get the proportions of G:
foo <- function(x) base.freq(x)["g"]
sw(woodmouse, 200, 200, FUN = foo, rowAverage = TRUE)
## a simulated example with the default method:
x <- runif(100)
pos <- sort(sample(1e6, 100))
resx <- sw(x, w = 2e4, s = 5e3, POS = pos, L = 1e6)
plot(resx, show.ranges = TRUE, x.scaling = 1e6, xlab = "Position (Mb)")
Example output
Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
Registered S3 method overwritten by 'spdep':
method from
plot.mst ape
/// adegenet 2.1.3 is loaded ////////////
> overview: '?adegenet'
> tutorials/doc/questions: 'adegenetWeb()'
> bug reports/feature requests: adegenetIssues()
Registered S3 method overwritten by 'pegas':
method from
print.amova ade4
Attaching package: ‘pegas’
The following object is masked from ‘package:ade4’:
amova
The following object is masked from ‘package:ape’:
mst
[1,100] [51,150] [101,200] [151,250] [201,300] [251,350] [301,400]
No305 0.3877551 0.40 0.3900000 0.3900000 0.36 0.35 0.40
No304 0.3800000 0.39 0.3800000 0.3800000 0.35 0.33 0.38
No306 0.3700000 0.39 0.3800000 0.3800000 0.35 0.33 0.38
No0906S 0.3700000 0.38 0.3800000 0.3800000 0.35 0.31 0.36
No0908S 0.3800000 0.40 0.3800000 0.3800000 0.36 0.34 0.38
No0909S 0.3900000 0.41 0.3800000 0.3900000 0.36 0.36 0.41
No0910S 0.3500000 0.39 0.3900000 0.3800000 0.35 0.32 0.37
No0912S 0.3900000 0.41 0.3800000 0.3800000 0.36 0.35 0.39
No0913S 0.3800000 0.39 0.3800000 0.3900000 0.36 0.32 0.37
No1103S 0.3800000 0.41 0.3800000 0.3800000 0.35 0.34 0.39
No1007S 0.3900000 0.41 0.3800000 0.3900000 0.36 0.36 0.41
No1114S 0.4000000 0.40 0.3939394 0.3939394 0.35 0.35 0.40
No1202S 0.3600000 0.39 0.3900000 0.3900000 0.36 0.32 0.37
No1206S 0.3700000 0.39 0.3800000 0.3800000 0.36 0.34 0.38
No1208S 0.4020619 0.41 0.3800000 0.4000000 0.37 0.36 0.41
[351,450] [401,500] [451,550] [501,600] [551,650] [601,700] [651,750]
No305 0.3636364 0.3838384 0.43 0.41 0.43 0.35 0.34
No304 0.3673469 0.3775510 0.41 0.39 0.42 0.35 0.35
No306 0.3600000 0.3700000 0.41 0.39 0.42 0.35 0.34
No0906S 0.3600000 0.3800000 0.42 0.39 0.42 0.34 0.33
No0908S 0.3700000 0.3800000 0.42 0.40 0.42 0.35 0.34
No0909S 0.3600000 0.3900000 0.42 0.38 0.42 0.35 0.34
No0910S 0.3600000 0.3800000 0.42 0.39 0.42 0.36 0.35
No0912S 0.3600000 0.3800000 0.43 0.40 0.42 0.36 0.35
No0913S 0.3600000 0.3700000 0.41 0.39 0.42 0.36 0.36
No1103S 0.3600000 0.3800000 0.42 0.39 0.42 0.35 0.34
No1007S 0.3600000 0.3900000 0.42 0.38 0.42 0.35 0.34
No1114S 0.3600000 0.3900000 0.41 0.38 0.42 0.36 0.35
No1202S 0.3600000 0.3800000 0.42 0.39 0.42 0.36 0.35
No1206S 0.3600000 0.3800000 0.42 0.39 0.42 0.35 0.35
No1208S 0.3700000 0.4000000 0.42 0.38 0.42 0.35 0.34
[701,800] [751,850] [801,900] [851,950] [901,965]
No305 0.4400000 0.4200000 0.38 0.40 0.4153846
No304 0.4500000 0.4400000 0.40 0.40 0.4218750
No306 0.4387755 0.4387755 0.40 0.40 0.4000000
No0906S 0.4400000 0.4300000 0.39 0.40 0.3934426
No0908S 0.4400000 0.4300000 0.39 0.40 0.4262295
No0909S 0.4400000 0.4300000 0.40 0.41 0.4262295
No0910S 0.4400000 0.4300000 0.39 0.40 0.4262295
No0912S 0.4400000 0.4200000 0.38 0.40 0.4262295
No0913S 0.4500000 0.4400000 0.40 0.40 0.4262295
No1103S 0.4400000 0.4200000 0.38 0.40 0.4262295
No1007S 0.4400000 0.4300000 0.40 0.41 0.4262295
No1114S 0.4400000 0.4300000 0.39 0.41 0.4426230
No1202S 0.4400000 0.4300000 0.39 0.40 0.4262295
No1206S 0.4500000 0.4300000 0.39 0.40 0.4262295
No1208S 0.4400000 0.4300000 0.40 0.41 0.4262295
attr(,"class")
[1] "sw"
[1,200] [201,400] [401,600] [601,800] [801,965]
No305 0.3888889 0.380 0.3969849 0.3950000 0.3939394
No304 0.3800000 0.365 0.3838384 0.4000000 0.4085366
No306 0.3750000 0.365 0.3800000 0.3939394 0.4000000
No0906S 0.3750000 0.355 0.3850000 0.3900000 0.3913043
No0908S 0.3800000 0.370 0.3900000 0.3950000 0.4037267
No0909S 0.3850000 0.385 0.3850000 0.3950000 0.4099379
No0910S 0.3700000 0.360 0.3850000 0.4000000 0.4037267
No0912S 0.3850000 0.375 0.3900000 0.4000000 0.3975155
No0913S 0.3800000 0.365 0.3800000 0.4050000 0.4099379
No1103S 0.3800000 0.370 0.3850000 0.3950000 0.3975155
No1007S 0.3850000 0.385 0.3850000 0.3950000 0.4099379
No1114S 0.3961039 0.375 0.3850000 0.4000000 0.4099379
No1202S 0.3750000 0.365 0.3850000 0.4000000 0.4037267
No1206S 0.3750000 0.370 0.3850000 0.4000000 0.4037267
No1208S 0.3908629 0.390 0.3900000 0.3950000 0.4099379
attr(,"class")
[1] "sw"
[1,200] [201,400] [401,600] [601,800] [801,965]
0.3811462 0.3716667 0.3860527 0.3972648 0.4035449
attr(,"class")
[1] "sw"
[1,200] [201,400] [401,600] [601,800] [801,965]
0.08816548 0.18900000 0.14581248 0.10507005 0.09563067
attr(,"class")
[1] "sw"
pegas documentation built on Dec. 16, 2021, 5:09 p.m.
R Package Documentation
Browse R Packages
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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 Details Value Author(s) Examples
Description
Applies a function over a matrix or a vector using sliding
windows. sw is a generic function with a method for
"DNAbin" matrices.
Usage
1 2 3 4 5 6 7 8 9 10 11 | sw(x, width, step, ...)
## Default S3 method:
sw(x, width = 100, step = 50, POS = NULL,
FUN = mean, out.of.pos = NA_real_, na.rm = TRUE, L = NULL, ...)
## S3 method for class 'DNAbin'
sw(x, width = 100, step = 50, FUN = GC.content,
rowAverage = FALSE, quiet = TRUE, ...)
## S3 method for class 'sw'
plot(x, type = "l", xlab = "Position", x.scaling = 1,
show.ranges = FALSE, col.ranges = "blue",
lty.ranges = 1, lwd.ranges = 1, ...)
|
Arguments
x |
a vector or a matrix. |
width |
an integer giving the window width. |
step |
an integer giving the step separating successive windows. |
POS |
a numeric vector giving the positions of the sites. |
FUN |
the function to be applied to the windows. |
rowAverage |
a logical value: if |
out.of.pos |
the values used for the sites which are not in
|
na.rm |
option passed to |
L |
the length of the chromosome (or sequence). If not given,
this is largest value in |
quiet |
a logical value: if |
type |
the type of plotting (see |
xlab |
the label under the x-axis. |
x.scaling |
the scaling of the x-axis. |
show.ranges |
a logical value specifying whether to show the
ranges of the windows with horizontal segments (ignored with a
warning if |
col.ranges, lty.ranges, lwd.ranges |
arguments to modify the
appearance of the above segments (see |
... |
further arguments passed to and from methods. |
Details
FUN should return a single value.
x should be a matrix for the "DNAbin" method, or a
vector for the default one.
For the default method, the vector x is expanded into a vector
of length L (see above on how this value is found) and the
positions which are not in POS are filled with the value given
in out.of.pos. The resulting vector is then analysed with the
function FUN which must have an option na.rm. If the
function you want to use does not have this option, you can use
something like FUN = function(x, na.rm = TRUE)
foo(x[!is.na(x)]), replacing ‘foo’ by the name of your function. You
may also include more control on the handling of missing data.
Value
a matrix or a vector (if rowAverage = TRUE).
Author(s)
Emmanuel Paradis
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | data(woodmouse)
sw(woodmouse)
sw(woodmouse, 200, 200)
sw(woodmouse, 200, 200, rowAverage = TRUE)
## to get the proportions of G:
foo <- function(x) base.freq(x)["g"]
sw(woodmouse, 200, 200, FUN = foo, rowAverage = TRUE)
## a simulated example with the default method:
x <- runif(100)
pos <- sort(sample(1e6, 100))
resx <- sw(x, w = 2e4, s = 5e3, POS = pos, L = 1e6)
plot(resx, show.ranges = TRUE, x.scaling = 1e6, xlab = "Position (Mb)")
|
Example output
Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
Registered S3 method overwritten by 'spdep':
method from
plot.mst ape
/// adegenet 2.1.3 is loaded ////////////
> overview: '?adegenet'
> tutorials/doc/questions: 'adegenetWeb()'
> bug reports/feature requests: adegenetIssues()
Registered S3 method overwritten by 'pegas':
method from
print.amova ade4
Attaching package: ‘pegas’
The following object is masked from ‘package:ade4’:
amova
The following object is masked from ‘package:ape’:
mst
[1,100] [51,150] [101,200] [151,250] [201,300] [251,350] [301,400]
No305 0.3877551 0.40 0.3900000 0.3900000 0.36 0.35 0.40
No304 0.3800000 0.39 0.3800000 0.3800000 0.35 0.33 0.38
No306 0.3700000 0.39 0.3800000 0.3800000 0.35 0.33 0.38
No0906S 0.3700000 0.38 0.3800000 0.3800000 0.35 0.31 0.36
No0908S 0.3800000 0.40 0.3800000 0.3800000 0.36 0.34 0.38
No0909S 0.3900000 0.41 0.3800000 0.3900000 0.36 0.36 0.41
No0910S 0.3500000 0.39 0.3900000 0.3800000 0.35 0.32 0.37
No0912S 0.3900000 0.41 0.3800000 0.3800000 0.36 0.35 0.39
No0913S 0.3800000 0.39 0.3800000 0.3900000 0.36 0.32 0.37
No1103S 0.3800000 0.41 0.3800000 0.3800000 0.35 0.34 0.39
No1007S 0.3900000 0.41 0.3800000 0.3900000 0.36 0.36 0.41
No1114S 0.4000000 0.40 0.3939394 0.3939394 0.35 0.35 0.40
No1202S 0.3600000 0.39 0.3900000 0.3900000 0.36 0.32 0.37
No1206S 0.3700000 0.39 0.3800000 0.3800000 0.36 0.34 0.38
No1208S 0.4020619 0.41 0.3800000 0.4000000 0.37 0.36 0.41
[351,450] [401,500] [451,550] [501,600] [551,650] [601,700] [651,750]
No305 0.3636364 0.3838384 0.43 0.41 0.43 0.35 0.34
No304 0.3673469 0.3775510 0.41 0.39 0.42 0.35 0.35
No306 0.3600000 0.3700000 0.41 0.39 0.42 0.35 0.34
No0906S 0.3600000 0.3800000 0.42 0.39 0.42 0.34 0.33
No0908S 0.3700000 0.3800000 0.42 0.40 0.42 0.35 0.34
No0909S 0.3600000 0.3900000 0.42 0.38 0.42 0.35 0.34
No0910S 0.3600000 0.3800000 0.42 0.39 0.42 0.36 0.35
No0912S 0.3600000 0.3800000 0.43 0.40 0.42 0.36 0.35
No0913S 0.3600000 0.3700000 0.41 0.39 0.42 0.36 0.36
No1103S 0.3600000 0.3800000 0.42 0.39 0.42 0.35 0.34
No1007S 0.3600000 0.3900000 0.42 0.38 0.42 0.35 0.34
No1114S 0.3600000 0.3900000 0.41 0.38 0.42 0.36 0.35
No1202S 0.3600000 0.3800000 0.42 0.39 0.42 0.36 0.35
No1206S 0.3600000 0.3800000 0.42 0.39 0.42 0.35 0.35
No1208S 0.3700000 0.4000000 0.42 0.38 0.42 0.35 0.34
[701,800] [751,850] [801,900] [851,950] [901,965]
No305 0.4400000 0.4200000 0.38 0.40 0.4153846
No304 0.4500000 0.4400000 0.40 0.40 0.4218750
No306 0.4387755 0.4387755 0.40 0.40 0.4000000
No0906S 0.4400000 0.4300000 0.39 0.40 0.3934426
No0908S 0.4400000 0.4300000 0.39 0.40 0.4262295
No0909S 0.4400000 0.4300000 0.40 0.41 0.4262295
No0910S 0.4400000 0.4300000 0.39 0.40 0.4262295
No0912S 0.4400000 0.4200000 0.38 0.40 0.4262295
No0913S 0.4500000 0.4400000 0.40 0.40 0.4262295
No1103S 0.4400000 0.4200000 0.38 0.40 0.4262295
No1007S 0.4400000 0.4300000 0.40 0.41 0.4262295
No1114S 0.4400000 0.4300000 0.39 0.41 0.4426230
No1202S 0.4400000 0.4300000 0.39 0.40 0.4262295
No1206S 0.4500000 0.4300000 0.39 0.40 0.4262295
No1208S 0.4400000 0.4300000 0.40 0.41 0.4262295
attr(,"class")
[1] "sw"
[1,200] [201,400] [401,600] [601,800] [801,965]
No305 0.3888889 0.380 0.3969849 0.3950000 0.3939394
No304 0.3800000 0.365 0.3838384 0.4000000 0.4085366
No306 0.3750000 0.365 0.3800000 0.3939394 0.4000000
No0906S 0.3750000 0.355 0.3850000 0.3900000 0.3913043
No0908S 0.3800000 0.370 0.3900000 0.3950000 0.4037267
No0909S 0.3850000 0.385 0.3850000 0.3950000 0.4099379
No0910S 0.3700000 0.360 0.3850000 0.4000000 0.4037267
No0912S 0.3850000 0.375 0.3900000 0.4000000 0.3975155
No0913S 0.3800000 0.365 0.3800000 0.4050000 0.4099379
No1103S 0.3800000 0.370 0.3850000 0.3950000 0.3975155
No1007S 0.3850000 0.385 0.3850000 0.3950000 0.4099379
No1114S 0.3961039 0.375 0.3850000 0.4000000 0.4099379
No1202S 0.3750000 0.365 0.3850000 0.4000000 0.4037267
No1206S 0.3750000 0.370 0.3850000 0.4000000 0.4037267
No1208S 0.3908629 0.390 0.3900000 0.3950000 0.4099379
attr(,"class")
[1] "sw"
[1,200] [201,400] [401,600] [601,800] [801,965]
0.3811462 0.3716667 0.3860527 0.3972648 0.4035449
attr(,"class")
[1] "sw"
[1,200] [201,400] [401,600] [601,800] [801,965]
0.08816548 0.18900000 0.14581248 0.10507005 0.09563067
attr(,"class")
[1] "sw"
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