summary.bioCond: Summarize a 'bioCond' Object

In MAnorm2: Tools for Normalizing and Comparing ChIP-seq Samples

Summarize a bioCond Object

Description

The method produces an object that summarizes the data and fit information of mean-variance dependence (if available) stored in a bioCond object.

Usage

## S3 method for class 'bioCond'
summary(object, ...)

Arguments

object	A bioCond object.
...	Arguments passed from other methods.

Details

This function implements the summary method for the "bioCond" class.

Value

The method returns an object of class "summaryBioCond", for which a specialized print method has been defined.

See Also

bioCond for creating a bioCond object. fitMeanVarCurve for fitting a mean-variance curve on bioCond objects.

Examples

data(H3K27Ac, package = "MAnorm2")
attr(H3K27Ac, "metaInfo")

## Summarize bioConds that correspond to individuals.

# Perform the MA normalization and construct bioConds to represent
# individuals.
norm <- normalize(H3K27Ac, 4, 9)
norm <- normalize(norm, 5:6, 10:11)
norm <- normalize(norm, 7:8, 12:13)
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)

# Summarize these bioConds.
summary(conds[[1]])
summary(conds[[2]])
summary(conds[[3]])
str(summary(conds[[3]]))

# Summarize these bioConds after fitting a mean-variance curve for them.
conds <- fitMeanVarCurve(conds, method = "parametric", occupy.only = TRUE)
summary(conds[[1]])
summary(conds[[2]])
summary(conds[[3]])
str(summary(conds[[3]]))

MAnorm2 documentation built on Oct. 29, 2022, 1:12 a.m.