counts: counts(PAC)

In Danis102/seqpac: Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts

counts(PAC)

Description

Access the raw counts table in S4 PAC

Usage

counts(object)

## S4 method for signature 'PAC'
counts(object)

## S4 replacement method for signature 'PAC,data.frame'
counts(object) <- value

Arguments

object	A S4 PAC-object containing Pheno, Anno and Counts tables. Can be generated by the 'PAC generation' family of functions, for example see ?make_counts.
value	Data.frame having the same column names as row names in Pheno (sample ID) and row names as row names in Anno (sequences).

Value

The Counts data frame table from a PAC-object.

Updated S4 PAC-object.

See Also

Other PAC methods: anno(), names,PAC-method, norm(), pheno(), show.PAC(), summary()

Examples

load(system.file("extdata", "drosophila_sRNA_pac_filt_anno.Rdata", 
                  package = "seqpac", mustWork = TRUE))

# extra fuctionality with s4 PAC-object:
names(pac)
length(pac)
nrow(pac)
ncol(pac)
rownames(pac)
colnames(pac)
pheno(pac) 
head(anno(pac))
head(counts(pac))
head(norm(pac)$cpm)

Danis102/seqpac documentation built on Aug. 26, 2023, 10:15 a.m.