print.summaryBioCond: Print a 'summaryBioCond' Object

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

Print a summaryBioCond Object

Description

This function prints the summary result of a bioCond object.

Usage

## S3 method for class 'summaryBioCond'
print(x, ...)

Arguments

x	An object of class "summaryBioCond", typically obtained by passing a bioCond object to the summary function.
...	Arguments passed from other methods.

Details

This function implements the print method for the "summaryBioCond" class.

Value

The function returns x invisibly.

See Also

bioCond for creating a bioCond object; summary.bioCond for summarizing a bioCond object.

Examples

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

## Print summary results of 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)

# Print summary results of these bioConds.
print(summary(conds[[1]]))
print(summary(conds[[2]]))
print(summary(conds[[3]]))

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

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