PAC_norm: Generates normalized values from a PAC object

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

Generates normalized values from a PAC object

Description

PAC_norm generates normalized values from a PAC object

Usage

PAC_norm(PAC, norm = "cpm", merge_pac = TRUE)

Arguments

PAC	PAC-list object containing an Anno data.frame with sequences as row names and a Count table with raw counts.
norm	Character indicating what type of normalization method that should be applied to the counts(PAC). If norm="cpm", counts per million reads is returned. Each sequence is then divided against the total number of counts in a given sample. If norm="vst", counts(PAC) will be imported into the varianceStabilizingTransformation function in the DESeq2-package with the options blind=TRUE and fitType="mean". If norm="rlog", counts(PAC) will instead be imported into the rlog function also available in DESeq2-package (options blind=TRUE and fitType="mean") for a log2 transformed version of vst, and is more robust to varying library sizes.
merge_pac	logical whether the normalized table should be returned and stored in the norm(PAC) 'folder' of the provided PAC object (TRUE) or be returned as a data frame.

Details

Using the counts in a PAC object to generate normalized values in a data.frame with the same rownames as in the original PAC object

Value

A normalized count table, or if pac_merge=TRUE, a PAC object with normalized counts table added to the norm folder (norm(PAC)).

See Also

https://github.com/Danis102 for updates on the current package.

Other PAC analysis: PAC_covplot(), PAC_deseq(), PAC_filter(), PAC_filtsep(), PAC_gtf(), PAC_jitter(), PAC_mapper(), PAC_nbias(), PAC_pca(), PAC_pie(), PAC_saturation(), PAC_sizedist(), PAC_stackbar(), PAC_summary(), PAC_trna(), as.PAC(), filtsep_bin(), map_rangetype(), tRNA_class()

Examples

load(system.file("extdata", "drosophila_sRNA_pac_filt_anno.Rdata", 
                  package = "seqpac", mustWork = TRUE))
pac_norm  <- PAC_norm(pac, norm="cpm") 
df_norm <- PAC_norm(pac, norm = "vst", merge_pac = FALSE)

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