Title: | Probabilistic inference of ChIP-seq |
---|---|
Description: | Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. |
Authors: | Xuekui Zhang <[email protected]>, Raphael Gottardo <[email protected]> |
Maintainer: | Renan Sauteraud <[email protected]> |
License: | Artistic-2.0 |
Version: | 2.51.0 |
Built: | 2024-10-31 04:54:10 UTC |
Source: | https://github.com/bioc/PICS |
Reads a bam file using Rsamtools
and extract the reads for each chromosome.
bam2gr(bamFile, chr = NULL, PE = FALSE, verbose = FALSE)
bam2gr(bamFile, chr = NULL, PE = FALSE, verbose = FALSE)
bamFile |
A |
chr |
A |
PE |
A |
verbose |
A |
A GRanges
of all the reads for each chromosome.
The user might encounter a memory allocation error when using bam
files of bigger sizes. Splitting the file by chromosome before calling bam2gr
will solve this issue.
For Paired-End data, non matched reads are discarded.
segmentPICS
Identify candidate regions from paired-end sequencing data.
candidate.region(PE.RD, islandDepth, min_cut, max_cut)
candidate.region(PE.RD, islandDepth, min_cut, max_cut)
PE.RD |
A |
islandDepth |
A |
min_cut |
A |
max_cut |
A |
Export a PICS object to GRanges
makeGRangesOutput( obj, type = "fixed", length = 100, filter = list(delta = c(0, Inf), se = c(0, Inf), sigmaSqF = c(0, Inf), sigmaSqR = c(0, Inf), score = c(0, Inf)) )
makeGRangesOutput( obj, type = "fixed", length = 100, filter = list(delta = c(0, Inf), se = c(0, Inf), sigmaSqF = c(0, Inf), sigmaSqR = c(0, Inf), score = c(0, Inf)) )
obj |
A |
type |
A |
length |
A |
filter |
A |
A GRanges
object.
PICS
This object contains Estimation of binding site positions and has the following slots: segReadsList, dataType.
PICS( segReadsList, dataType = NULL, paraEM = NULL, paraPrior = NULL, nCores = 1 )
PICS( segReadsList, dataType = NULL, paraEM = NULL, paraPrior = NULL, nCores = 1 )
segReadsList |
This object contains segmentation of Genome |
dataType |
A |
paraEM |
A |
paraPrior |
A |
nCores |
An |
An object of class picsList
containing the estimated binding
site positions.
This object is used to gather all parameters from fitting PICS to a single candidate region.
## S4 method for signature 'pics' show(object) ## S4 method for signature 'pics' minRange(x) ## S4 method for signature 'pics' maxRange(x) ## S4 method for signature 'pics' score(x) ## S4 method for signature 'pics' scoreReverse(x) ## S4 method for signature 'pics' scoreForward(x) ## S4 method for signature 'pics' chromosome(x) ## S4 method for signature 'pics' se(x) ## S4 method for signature 'pics' seF(x) ## S4 method for signature 'pics' seR(x) ## S4 method for signature 'pics' sigmaSqF(x) ## S4 method for signature 'pics' sigmaSqR(x) ## S4 method for signature 'pics' delta(x) ## S4 method for signature 'pics' mu(x) ## S4 method for signature 'pics' w(x) ## S4 method for signature 'pics' K(x) ## S4 method for signature 'pics' code(x) ## S4 method for signature 'pics' summary(object)
## S4 method for signature 'pics' show(object) ## S4 method for signature 'pics' minRange(x) ## S4 method for signature 'pics' maxRange(x) ## S4 method for signature 'pics' score(x) ## S4 method for signature 'pics' scoreReverse(x) ## S4 method for signature 'pics' scoreForward(x) ## S4 method for signature 'pics' chromosome(x) ## S4 method for signature 'pics' se(x) ## S4 method for signature 'pics' seF(x) ## S4 method for signature 'pics' seR(x) ## S4 method for signature 'pics' sigmaSqF(x) ## S4 method for signature 'pics' sigmaSqR(x) ## S4 method for signature 'pics' delta(x) ## S4 method for signature 'pics' mu(x) ## S4 method for signature 'pics' w(x) ## S4 method for signature 'pics' K(x) ## S4 method for signature 'pics' code(x) ## S4 method for signature 'pics' summary(object)
object , x
|
A |
show,pics-method
: show method
minRange,pics-method
: Get start of range
maxRange,pics-method
: Get end of range
score,pics-method
: Score accessor.
scoreReverse,pics-method
: Reverse score accessor.
scoreForward,pics-method
: Forward score accessor.
chromosome,pics-method
: Chromosome accessor
se,pics-method
: se accessor
seF,pics-method
: Forward se accessor
seR,pics-method
: Reverse se accessor
sigmaSqF,pics-method
: sigmaSqF accessor
sigmaSqR,pics-method
: sigmaSqR accessor
delta,pics-method
: delta accessor
mu,pics-method
: mu accessor
w,pics-method
: w accessor
K,pics-method
: K accessor
code,pics-method
: Error code accessor
summary,pics-method
: Summary of the object
estimates
A list containing all parameters estimates as well as standard errors.
Nmerged
The number of binding events that were merged; binding events that overlap are merged.
converge
A logical
value indicating whether the EM algorithm has converged.
chr
The candidate region's chromosome.
score
Score of the binding event
scoreF
Forward score of the binding event.
scoreR
Reverse score of the binding event.
range
Genomic ranges.
These generics are used in methods of pics
, picsError
and
picsList
classes. See class help pages for method documentation.
minRange(x, ...) maxRange(x, ...) score(x, ...) scoreReverse(x, ...) scoreForward(x, ...) chromosome(x, ...) se(x, ...) seF(x, ...) seR(x, ...) sigmaSqF(x, ...) sigmaSqR(x, ...) delta(x, ...) mu(x, ...) w(x, ...) K(x, ...) code(x, ...) ## S4 method for signature 'data.frame' score(x) ## S4 method for signature 'data.frame' scoreReverse(x) ## S4 method for signature 'data.frame' scoreForward(x) ## S4 method for signature 'data.frame' chromosome(x) ## S4 method for signature 'data.frame' se(x) ## S4 method for signature 'data.frame' seF(x) ## S4 method for signature 'data.frame' seR(x) ## S4 method for signature 'data.frame' sigmaSqF(x) ## S4 method for signature 'data.frame' sigmaSqR(x) ## S4 method for signature 'data.frame' delta(x) ## S4 method for signature 'data.frame' mu(x)
minRange(x, ...) maxRange(x, ...) score(x, ...) scoreReverse(x, ...) scoreForward(x, ...) chromosome(x, ...) se(x, ...) seF(x, ...) seR(x, ...) sigmaSqF(x, ...) sigmaSqR(x, ...) delta(x, ...) mu(x, ...) w(x, ...) K(x, ...) code(x, ...) ## S4 method for signature 'data.frame' score(x) ## S4 method for signature 'data.frame' scoreReverse(x) ## S4 method for signature 'data.frame' scoreForward(x) ## S4 method for signature 'data.frame' chromosome(x) ## S4 method for signature 'data.frame' se(x) ## S4 method for signature 'data.frame' seF(x) ## S4 method for signature 'data.frame' seR(x) ## S4 method for signature 'data.frame' sigmaSqF(x) ## S4 method for signature 'data.frame' sigmaSqR(x) ## S4 method for signature 'data.frame' delta(x) ## S4 method for signature 'data.frame' mu(x)
x , ...
|
Object and argumemts passed to the methods. |
minRange
: Start accessor
maxRange
: End accessor
score
: Score accessor
scoreReverse
: Reverse score accessor
scoreForward
: Forward score accesor
chromosome
: Chromosome accessor
se
: se accessor
seF
: Forward se accessor
seR
: Reverse se accessor
sigmaSqF
: sigmaSqF accessor
sigmaSqR
: sigmaSqR accessor
delta
: delta accessor
mu
: mu accessor
w
: w accessor
K
: K accessor
code
: Return error codes
score,data.frame-method
: Score accessor
scoreReverse,data.frame-method
: Reverse score accessor
scoreForward,data.frame-method
: Forward score accessorse
chromosome,data.frame-method
: chromosome accessor
se,data.frame-method
: se accessor
seF,data.frame-method
: seF accessor
seR,data.frame-method
: seR accessor
sigmaSqF,data.frame-method
: sigmaSqF accessor
sigmaSqR,data.frame-method
: sigmaSqR accessor
delta,data.frame-method
: delta accessor
mu,data.frame-method
: mu accessor
This class is used in cases when the algorithm does not converge.
## S4 method for signature 'picsError' show(object) ## S4 method for signature 'picsError' minRange(x) ## S4 method for signature 'picsError' maxRange(x) ## S4 method for signature 'picsError' score(x) ## S4 method for signature 'picsError' scoreReverse(x) ## S4 method for signature 'picsError' scoreForward(x) ## S4 method for signature 'picsError' chromosome(x) ## S4 method for signature 'picsError' se(x) ## S4 method for signature 'picsError' seF(x) ## S4 method for signature 'picsError' seR(x) ## S4 method for signature 'picsError' sigmaSqF(x) ## S4 method for signature 'picsError' sigmaSqR(x) ## S4 method for signature 'picsError' delta(x) ## S4 method for signature 'picsError' mu(x) ## S4 method for signature 'picsError' w(x) ## S4 method for signature 'picsError' K(x) ## S4 method for signature 'picsError' code(x)
## S4 method for signature 'picsError' show(object) ## S4 method for signature 'picsError' minRange(x) ## S4 method for signature 'picsError' maxRange(x) ## S4 method for signature 'picsError' score(x) ## S4 method for signature 'picsError' scoreReverse(x) ## S4 method for signature 'picsError' scoreForward(x) ## S4 method for signature 'picsError' chromosome(x) ## S4 method for signature 'picsError' se(x) ## S4 method for signature 'picsError' seF(x) ## S4 method for signature 'picsError' seR(x) ## S4 method for signature 'picsError' sigmaSqF(x) ## S4 method for signature 'picsError' sigmaSqR(x) ## S4 method for signature 'picsError' delta(x) ## S4 method for signature 'picsError' mu(x) ## S4 method for signature 'picsError' w(x) ## S4 method for signature 'picsError' K(x) ## S4 method for signature 'picsError' code(x)
object , x
|
A |
show,picsError-method
: show method
minRange,picsError-method
: Get start of range
maxRange,picsError-method
: Get end of range
score,picsError-method
: Score accessor.
scoreReverse,picsError-method
: Reverse score accessor.
scoreForward,picsError-method
: Forward score accessor.
chromosome,picsError-method
: Chromosome accessor
se,picsError-method
: se accessor
seF,picsError-method
: Forward se accessor
seR,picsError-method
: Reverse se accessor
sigmaSqF,picsError-method
: sigmaSqF accessor
sigmaSqR,picsError-method
: sigmaSqR accessor
delta,picsError-method
: delta accessor
mu,picsError-method
: mu accessor
w,picsError-method
: w accessor
K,picsError-method
: K accessor
code,picsError-method
: Error code accessor
errorCode
The error code for debugging.
Estimate the false detection rate for an object of class pics
or
picsList
.
picsFDR( picsIP, picsCont, filter = list(delta = c(0, Inf), se = c(0, Inf), sigmaSqF = c(0, Inf), sigmaSqR = c(0, Inf)) )
picsFDR( picsIP, picsCont, filter = list(delta = c(0, Inf), se = c(0, Inf), sigmaSqF = c(0, Inf), sigmaSqR = c(0, Inf)) )
picsIP |
An object of class |
picsCont |
An object of class |
filter |
A
|
A data.frame
with the following columns: FDR, score, N
picsList pics
List of PICS objects
## S4 method for signature 'picsList' show(object) ## S4 method for signature 'picsList' minRange(x) ## S4 method for signature 'picsList' maxRange(x) ## S4 method for signature 'picsList' score(x) ## S4 method for signature 'picsList' scoreReverse(x) ## S4 method for signature 'picsList' scoreForward(x) ## S4 method for signature 'picsList' chromosome(x) ## S4 method for signature 'picsList' se(x) ## S4 method for signature 'picsList' seF(x) ## S4 method for signature 'picsList' seR(x) ## S4 method for signature 'picsList' sigmaSqF(x) ## S4 method for signature 'picsList' sigmaSqR(x) ## S4 method for signature 'picsList' delta(x) ## S4 method for signature 'picsList' mu(x) ## S4 method for signature 'picsList' w(x) ## S4 method for signature 'picsList' K(x) ## S4 method for signature 'picsList' code(x) ## S4 method for signature 'picsList' length(x) ## S4 method for signature 'picsList' summary(object) ## S4 method for signature 'picsList,ANY,ANY,ANY' x[i, j, ..., drop = FALSE] ## S4 method for signature 'picsList,ANY,ANY' x[[i, j, ..., exact = TRUE]]
## S4 method for signature 'picsList' show(object) ## S4 method for signature 'picsList' minRange(x) ## S4 method for signature 'picsList' maxRange(x) ## S4 method for signature 'picsList' score(x) ## S4 method for signature 'picsList' scoreReverse(x) ## S4 method for signature 'picsList' scoreForward(x) ## S4 method for signature 'picsList' chromosome(x) ## S4 method for signature 'picsList' se(x) ## S4 method for signature 'picsList' seF(x) ## S4 method for signature 'picsList' seR(x) ## S4 method for signature 'picsList' sigmaSqF(x) ## S4 method for signature 'picsList' sigmaSqR(x) ## S4 method for signature 'picsList' delta(x) ## S4 method for signature 'picsList' mu(x) ## S4 method for signature 'picsList' w(x) ## S4 method for signature 'picsList' K(x) ## S4 method for signature 'picsList' code(x) ## S4 method for signature 'picsList' length(x) ## S4 method for signature 'picsList' summary(object) ## S4 method for signature 'picsList,ANY,ANY,ANY' x[i, j, ..., drop = FALSE] ## S4 method for signature 'picsList,ANY,ANY' x[[i, j, ..., exact = TRUE]]
object , x
|
A |
i , j , ... , drop , exact
|
Arguments passed to subset functions |
show,picsList-method
: show method
minRange,picsList-method
: Get start of range
maxRange,picsList-method
: Get end of range
score,picsList-method
: Score accessor.
scoreReverse,picsList-method
: Reverse score accessor.
scoreForward,picsList-method
: Forward score accessor.
chromosome,picsList-method
: Chromosome accessor
se,picsList-method
: se accessor
seF,picsList-method
: Forward se accessor
seR,picsList-method
: Reverse se accessor
sigmaSqF,picsList-method
: sigmaSqF accessor
sigmaSqR,picsList-method
: sigmaSqR accessor
delta,picsList-method
: delta accessor
mu,picsList-method
: mu accessor
w,picsList-method
: w accessor
K,picsList-method
: K accessor
code,picsList-method
: Error code accessor
length,picsList-method
: Return the length of the object
summary,picsList-method
: Summary of the object
[,picsList,ANY,ANY,ANY-method
: Subset list
[[,picsList,ANY,ANY-method
: Subset element
This method plots a curve showing the FDR as a function of the PICS scores.
## S4 method for signature 'picsList,picsList' plot(x, y, filter = NULL, h = 0.1, ...)
## S4 method for signature 'picsList,picsList' plot(x, y, filter = NULL, h = 0.1, ...)
x |
A |
y |
A |
filter |
A list of ranges for filtering regions based on |
h |
A value between 0 and 1, representing the desired FDR. This simply draws a horizontal line at the given value. |
... |
Further graphical parameters passed to the generic function |
PICS
Methods to plot pics
and segReads
objects and derived classes.
## S4 method for signature 'pics,segReads' plot( x, y, addKernel = FALSE, addNucleosome = FALSE, addSe = TRUE, main = NULL, ... ) ## S4 method for signature 'picsError,segReads' plot(x, y, addKernel = FALSE, main = NULL, ...) ## S4 method for signature 'picsList,segReadsList' plot( x, y, regionIndex = NULL, addKernel = FALSE, addNucleosome = FALSE, addSe = TRUE, main = NULL, ... )
## S4 method for signature 'pics,segReads' plot( x, y, addKernel = FALSE, addNucleosome = FALSE, addSe = TRUE, main = NULL, ... ) ## S4 method for signature 'picsError,segReads' plot(x, y, addKernel = FALSE, main = NULL, ...) ## S4 method for signature 'picsList,segReadsList' plot( x, y, regionIndex = NULL, addKernel = FALSE, addNucleosome = FALSE, addSe = TRUE, main = NULL, ... )
x , y
|
Objects |
addKernel |
Add kernel density estimate to the plot. |
addNucleosome |
Add a nucleosome track to the plot. |
addSe |
Add standard error to the plot. |
main |
Main title. |
... |
Arguments to be passed to the plot method. |
regionIndex |
Add region index to the plot. |
plot,pics,segReads-method
: Plot method for pics
and segReads
plot,picsError,segReads-method
: Plot method for picsError
and segReads
plot,picsList,segReadsList-method
: Plot method for picsList
and segReadsList
These two functions are part of the segmentation step for paired-end sequencing data and are exported to be used in PING
package.
Pre-process bidirectional aligned reads data from a single ChIP-Seq experiment to detect candidate regions with a minimum number of forward and reverse reads. These candidate regions will then be processed by PICS.
segmentPICS( data, dataC = NULL, map = NULL, minReads = 2, minReadsInRegion = 3, jitter = FALSE, dataType = "TF", maxLregion = 0, minLregion = 100 )
segmentPICS( data, dataC = NULL, map = NULL, minReads = 2, minReadsInRegion = 3, jitter = FALSE, dataType = "TF", maxLregion = 0, minLregion = 100 )
data |
A |
dataC |
A |
map |
A |
minReads |
A |
minReadsInRegion |
A |
jitter |
A |
dataType |
A |
maxLregion |
A |
minLregion |
A |
An object of class segReadsList
containing the results for all
pre-processed regions.
X. Zhang, G. Robertson, M. Krzywinski, K. Ning, A. Droit, S. Jones, and R. Gottardo, “PICS: Probabilistic Inference for ChIP-seq” arXiv, 0903.3206, 2009.
segReadsList
# Read data path<-system.file("extdata",package="PICS") ## Note that the col name for the chromosome needs to be space and not chr dataIP <- read.table(file.path(path, "Treatment_tags_chr21_sort.bed"), header=TRUE, colClasses = c("factor","integer","integer","factor")) dataIP <- as(dataIP, "GRanges") dataCont <- read.table(file.path(path, "Input_tags_chr21_sort.bed"), header=TRUE, colClasses = c("factor","integer","integer","factor")) dataCont <- as(dataCont, "GRanges") map <- read.table(file.path(path, "mapProfileShort"), header=TRUE, colClasses = c("factor","integer","integer","NULL")) map <- as(map, "GRanges") seg <- segmentPICS(dataIP, dataC = dataCont, map = map, minReads = 1)
# Read data path<-system.file("extdata",package="PICS") ## Note that the col name for the chromosome needs to be space and not chr dataIP <- read.table(file.path(path, "Treatment_tags_chr21_sort.bed"), header=TRUE, colClasses = c("factor","integer","integer","factor")) dataIP <- as(dataIP, "GRanges") dataCont <- read.table(file.path(path, "Input_tags_chr21_sort.bed"), header=TRUE, colClasses = c("factor","integer","integer","factor")) dataCont <- as(dataCont, "GRanges") map <- read.table(file.path(path, "mapProfileShort"), header=TRUE, colClasses = c("factor","integer","integer","NULL")) map <- as(map, "GRanges") seg <- segmentPICS(dataIP, dataC = dataCont, map = map, minReads = 1)
Pre-process bidirectional aligned reads data from a single ChIP-Seq
experiment to detect candidate regions with a minimum number of forward and
reverse reads. These candidate regions will then be processed by PICS
.
segReads(yF, yR, cF, cR, map, chr) segReadsList(List, paraSW, N, Nc) ## S4 method for signature 'segReads' show(object) ## S4 method for signature 'segReadsList' show(object) map(x, ...) ## S4 method for signature 'segReads' map(x) ## S4 method for signature 'segReadsList' map(x) ## S4 method for signature 'segReadsList' length(x) ## S4 method for signature 'segReadsList' summary(object) ## S4 method for signature 'segReads' summary(object) ## S4 method for signature 'segReadsList,ANY,ANY,ANY' x[i, j, ..., drop = FALSE] ## S4 method for signature 'segReadsList,ANY,ANY' x[[i, j, ..., exact = TRUE]]
segReads(yF, yR, cF, cR, map, chr) segReadsList(List, paraSW, N, Nc) ## S4 method for signature 'segReads' show(object) ## S4 method for signature 'segReadsList' show(object) map(x, ...) ## S4 method for signature 'segReads' map(x) ## S4 method for signature 'segReadsList' map(x) ## S4 method for signature 'segReadsList' length(x) ## S4 method for signature 'segReadsList' summary(object) ## S4 method for signature 'segReads' summary(object) ## S4 method for signature 'segReadsList,ANY,ANY,ANY' x[i, j, ..., drop = FALSE] ## S4 method for signature 'segReadsList,ANY,ANY' x[[i, j, ..., exact = TRUE]]
yF |
A |
yR |
A |
cF |
A |
cR |
A |
map |
A |
chr |
A |
List |
A |
paraSW |
A |
N |
A |
Nc |
A |
object , x
|
A |
i , j , ... , exact , drop
|
Additional arguments passed to subset methods. |
segReads
: segReads
Constructor
segReadsList
: segReadsList
Constructor
show,segReads-method
: show method
show,segReadsList-method
: show method
map
: map generic
map,segReads-method
: map method
map,segReadsList-method
: map method
length,segReadsList-method
: Return length of segReadsList
summary,segReadsList-method
: Summary method
summary,segReads-method
: Summary method
[,segReadsList,ANY,ANY,ANY-method
: Subset methods
[[,segReadsList,ANY,ANY-method
: Subset methods
segReads and segReadsList objects are not meant to be built via the
constructors. The constructors are used in segmentPICS
.
Perform genome segmentation depending
segReadsGeneric( data, dataC = NULL, map = NULL, minReads = 2, minReadsInRegion = 3, jitter = FALSE, maxLregion = 0, minLregion = 100, step = 20, width = 250, package = "PICS" )
segReadsGeneric( data, dataC = NULL, map = NULL, minReads = 2, minReadsInRegion = 3, jitter = FALSE, maxLregion = 0, minLregion = 100, step = 20, width = 250, package = "PICS" )
data |
A |
dataC |
A |
map |
A |
minReads |
A |
minReadsInRegion |
A |
jitter |
A |
maxLregion |
A |
minLregion |
A |
step |
A |
width |
A |
package |
A |
Class and methods for list of candidate regions from paired-end data
segReadsListPE(List, paraSW, N, NFm, NRm, Nc, NcFm, NcRm) ## S4 method for signature 'segReadsListPE,ANY,ANY,ANY' x[i, j, ..., drop = FALSE] ## S4 method for signature 'segReadsListPE,ANY,ANY' x[[i, j, ..., exact = TRUE]]
segReadsListPE(List, paraSW, N, NFm, NRm, Nc, NcFm, NcRm) ## S4 method for signature 'segReadsListPE,ANY,ANY,ANY' x[i, j, ..., drop = FALSE] ## S4 method for signature 'segReadsListPE,ANY,ANY' x[[i, j, ..., exact = TRUE]]
List |
A |
paraSW |
A |
N , NFm , NRm
|
Read counts in the data. |
Nc , NcFm , NcRm
|
Read counts in the control. |
x , i , j , ... , drop , exact
|
Arguments passed to subset methods |
segReadsListPE
: segReadsListPE
constructor.
[,segReadsListPE,ANY,ANY,ANY-method
: subset method
[[,segReadsListPE,ANY,ANY-method
: subset method
A segReadsPE object represents a single candoidate region, including all its informative reads and mappability profile.
segReadsPE(yF, yR, yFm, yRm, cF, cR, cFm, cRm, map, chr)
segReadsPE(yF, yR, yFm, yRm, cF, cR, cFm, cRm, map, chr)
yF |
A |
yR |
A |
yFm |
A |
yRm |
A |
cF |
A |
cR |
A |
cFm |
A |
cRm |
A |
map |
A |
chr |
A |
segReadsPE
: segReadsPE
constructor.
segReadsPE objects are not meant to be built via the
constructors. The constructors are used in segmentPICS
.
This function takes from 0 to 7 EM algorithm parameters as argument, check if they are valid and returns a list to be used in a call to PICS.
setParaEM( minK = 1, maxK = 15, tol = 1e-04, B = 100, mSelect = "BIC", mergePeaks = TRUE, mapCorrect = TRUE, dataType = NULL )
setParaEM( minK = 1, maxK = 15, tol = 1e-04, B = 100, mSelect = "BIC", mergePeaks = TRUE, mapCorrect = TRUE, dataType = NULL )
minK |
An |
maxK |
An |
tol |
A |
B |
An |
mSelect |
A |
mergePeaks |
A |
mapCorrect |
A |
dataType |
A |
A list
of parameters to be used in PICS
.
PICS setParaPrior
This function takes from 0 to 6 parameters as argument, check if they are valid and returns a list to be used in a call to PICS.
setParaPrior( xi = 200, rho = 1, alpha = 20, beta = 40000, lambda = 0, dMu = 0, dataType = NULL, PExi = 0 )
setParaPrior( xi = 200, rho = 1, alpha = 20, beta = 40000, lambda = 0, dMu = 0, dataType = NULL, PExi = 0 )
xi |
An |
rho |
An |
alpha |
An |
beta |
An |
lambda |
An |
dMu |
An |
dataType |
A character string. If a valid dataType is specified, use our suggested parameters. "MNase" or "sonicated" |
PExi |
A |
A list
of 6 parameters to be used in PICS
.
setParaEM PICS
# set prior for PICS data paraPrior <- setParaPrior() # set prior for sonicated data using our selected default parameters paraPrior <- setParaPrior(dataType="sonicated")
# set prior for PICS data paraPrior <- setParaPrior() # set prior for sonicated data using our selected default parameters paraPrior <- setParaPrior(dataType="sonicated")
Summarize segmentList objects into a data.frame
summarySeg(seg)
summarySeg(seg)
seg |
A |
A data.frame
. With
chr: Chromosome id
NF: Number of forward reads
NR: Number of reverse reads
L: Length of segment
min: Start location of segments
max: End location of segments