PAC_check: Checks PAC format

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

Checks PAC format

Description

PAC_check Quickly checks rownames in PAC.

Usage

PAC_check(PAC, sample_check = NULL, seq_check = NULL)

Arguments

PAC	PAC-list object.
sample_check	Can be provided either as a data frame or the name of a data frame in PAC. Will check both the row and column names of the object for identical sample names in PAC. A simple character vector can also be provided.
seq_check	Can be provided either as a data frame or the name of an data frame in PAC. Will check only the row names of the object for identical sequence names in PAC. A simple character vector can also be provided.

Details

Given a PAC object the function will cross check the rownames and colnames across Pheno, Anno and Counts.

Value

If PAC format is correct will return logical TRUE, else it will throw an error.

See Also

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

Other PAC generation: create_PAC(), make_PAC(), make_counts(), make_cutadapt(), make_pheno(), make_trim(), merge_lanes()

Examples

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

PAC_check(pac)  # TRUE

# Remove first row in Anno and check compatibility
new_Anno <- anno(pac)[-1,]
#PAC_check(pac, seq_check=new_Anno) # Error

# Add to pac an check
# anno(pac) <- new_Anno #error

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