cmbBioCond {MAnorm2} | R Documentation |
Combine a Set of bioCond
Objects into a Single bioCond
Description
Given a list of bioCond
objects, cmbBioCond
combines
them into a single bioCond
, by treating each bioCond
as an
individual ChIP-seq sample. This function is primarily used to handle
ChIP-seq samples associated with a hierarchical structure (see "Details"
for an example).
Usage
cmbBioCond(
conds,
occupy.num = 1,
name = "NA",
weight = NULL,
strMatrix = NULL,
meta.info = NULL
)
Arguments
conds |
A list of |
occupy.num |
For each interval, the minimum number of |
name |
Name of the constructed biological condition, used only for
demonstrating a |
weight |
A matrix or data frame specifying the relative precisions of
signal intensities of the constructed |
strMatrix |
An optional list of symmetric matrices specifying directly
the structure matrix of each genomic interval in the constructed
|
meta.info |
Optional extra information about the |
Details
Technically, cmbBioCond
treats each bioCond
object in
conds
as a ChIP-seq sample, taking the sample.mean
and
occupancy
fields stored in each bioCond
to represent its
signal intensities and occupancy indicators, respectively. Then, by grouping
these "samples", a new bioCond
object is constructed following the
exact routine as described in bioCond
. See
bioCond
also for a description of the structure of a
bioCond
object.
Notably, ChIP-seq samples contained in these bioCond
objects to be
combined are supposed to have been normalized to the same level, so that
these bioCond
s are comparable to each other. For this purpose, you
may choose to normalize the ChIP-seq samples involved all together via
normalize
, or to normalize the bioCond
objects to be
combined via normBioCond
.
cmbBioCond
is primarily used to deal with ChIP-seq samples sorted
into a hierarchical structure. For example, suppose ChIP-seq samples are
available for multiple male and female individuals, where each individual
is associated with several replicates. To call differential ChIP-seq signals
between males and females, two bioCond
objects representing these two
conditions need to be created. One way to do that is to select one ChIP-seq
sample as representative for each individual, and group male and female
samples, respectively. Alternatively, to leverage all available ChIP-seq
samples, a bioCond
object could be constructed for each individual,
consisting of the samples of him (her). Then, the bioCond
s of
male and female can be separately created by grouping the corresponding
individuals. See also "Examples" below.
Value
A bioCond
object, created by combining all the
supplied bioCond
objects.
See Also
bioCond
for creating a bioCond
object from a
set of ChIP-seq samples; normalize
for performing an MA
normalization on ChIP-seq samples; normBioCond
for
normalizing a set of bioCond
s; setWeight
for
modifying the structure matrices of a bioCond
object.
MAplot.bioCond
for creating an MA plot on two
bioCond
objects; summary.bioCond
for
summarizing a bioCond
.
fitMeanVarCurve
for modeling
the mean-variance dependence across intervals in bioCond
objects;
diffTest
for comparing two
bioCond
objects; aovBioCond
for comparing multiple
bioCond
objects; varTestBioCond
for calling
hypervariable and invariant intervals across ChIP-seq samples contained
in a bioCond
.
Examples
data(H3K27Ac, package = "MAnorm2")
attr(H3K27Ac, "metaInfo")
## Construct two bioConds comprised of the male and female individuals,
## respectively.
# First, normalize ChIP-seq samples separately for each individual (i.e.,
# cell line).
norm <- normalize(H3K27Ac, 4, 9)
norm <- normalize(norm, 5:6, 10:11)
norm <- normalize(norm, 7:8, 12:13)
# Then, construct separately a bioCond for each individual, and perform MA
# normalization on the resulting bioConds. Genomic intervals in sex
# chromosomes are not allowed to be common peak regions, since the
# individuals are of different genders.
conds <- list(GM12890 = bioCond(norm[4], norm[9], name = "GM12890"),
GM12891 = bioCond(norm[5:6], norm[10:11], name = "GM12891"),
GM12892 = bioCond(norm[7:8], norm[12:13], name = "GM12892"))
autosome <- !(H3K27Ac$chrom %in% c("chrX", "chrY"))
conds <- normBioCond(conds, common.peak.regions = autosome)
# Finally, group individuals into bioConds based on their genders.
female <- cmbBioCond(conds[c(1, 3)], name = "female")
male <- cmbBioCond(conds[2], name = "male")
summary(female)
summary(male)