PAC: S4 object for PAC

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

S4 object for PAC

Description

S4 version of the PAC object.

Usage

PAC(Pheno, Anno, Counts, norm, summary)

Arguments

Pheno	Phenotype data.frame table with sample ID as row names and where columns are variables associated with the samples. Can be generated using the make_pheno function.
Anno	Annotation data.frame table with unique sequences as row names and where columns are variables associated with the sequences.
Counts	Counts table (data.frame) with unique sequences as row names (identical to Anno) and where columns are sample ID (identical to row names for Pheno. Should contain raw counts and can be generated using the make_counts function.
norm	List of data.frames. May be regarded as a "folder" with normalized counts tables. The listed data.frames must have identical sequence names as Counts/Anno (rows) and sample IDs (columns) as Counts/Pheno. Can be generated using the PAC_norm function, but seqpac functions will attempt use any normalized table stored in norm that are in agreement with the above cafeterias.
summary	List of data.frames, just like norm, but contains summarized raw or normalized counts (e.g. means, standard errors, fold changes). Important, the listed data.frames must have identical sequence names as Counts/Anno (rows), but columns don't need sample IDs. Can be generated using the PAC_summary function, but seqpac functions will attempt use any summarized table stored in the summary "folder".

Details

Just like the S3 version, all sub-tables must have identical sequence (row) names. To extract tables from S4 objects, use the getter commands or use @ (e.g. PAC@Pheno) just like $ for the S3 version (e.g. pheno(PAC)). You may also use a coercion method, e.g. PAC_S3 <- as(PAC_S4, "list")

Holds up to 5 slots:

Pheno

data.frame > information about the samples

Anno

data.frame > sequences annotations

Counts

data.frame > sequence counts over samples

norm (optional)

list of data.frames > normalized counts

summary (optional)

list of data.frames > summarized counts or normalized counts

Value

Generates a S4 PAC-object.

Examples

load(system.file("extdata", "drosophila_sRNA_pac_filt_anno.Rdata", 
                  package = "seqpac", mustWork = TRUE))
                  
# check type
class(pac)
isS4(pac)
 
 
# Turns S4 PAC object into a S3
pac_s3 <- as(pac, "list")

# Turns S3 PAC object into a S4
pac_s4 <- as.PAC(pac_s3)

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