overview: overview(reanno)

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

overview(reanno)

Description

Access the overview table in a S4 reanno object

Usage

overview(object)

## S4 method for signature 'reanno'
overview(object)

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

Arguments

object	A S4 reanno-object containing an overview table.
value	Tibble data.frame with the same property as the Overview table of the reanno object, e.g. having the same names in seq column as row names (sequences) in the original PAC-object used to generate the reanno object. See examples and ?make_reanno for details.

Value

The overview table of a reanno-object as a tibble data.frame (class tbl_df, tbl, data.frame).

Updated reanno-object.

See Also

Other reanno methods: full()

Examples

######################################################### 
##### Create a reanno object

##  First load a PAC- object

 load(system.file("extdata", "drosophila_sRNA_pac_filt_anno.Rdata", 
                   package = "seqpac", mustWork = TRUE))
 anno(pac) <- anno(pac)[,1, drop = FALSE]
 
 
##  Then specify paths to fasta references
# If you are having problem see the vignette small RNA guide for more info.
 
 trna_path <- system.file("extdata/trna", "tRNA.fa", 
                          package = "seqpac", mustWork = TRUE)  
 rrna_path <- system.file("extdata/rrna", "rRNA.fa", 
                          package = "seqpac", mustWork = TRUE)
 
 ref_paths <- list(trna= trna_path, rrna= rrna_path)
 
##  Add output path of your choice.
# Here we use the R temporary folder depending on platform 
if(grepl("windows", .Platform$OS.type)){
 output <- paste0(tempdir(), "\\seqpac\\test")
}else{
 output <- paste0(tempdir(), "/seqpac/test")}

## Make sure it is empty (otherwise you will be prompted for a question)
out_fls  <- list.files(output, recursive=TRUE)
closeAllConnections()
suppressWarnings(file.remove(paste(output, out_fls, sep="/")))

##  Then map your PAC-object against the fasta references 
 map_reanno(pac, ref_paths=ref_paths, output_path=output,
               type="internal", mismatches=2,  import="biotype", 
               threads=2, keep_temp=FALSE)

##  Then generate a reanno-object of the temporary bowtie-files 
reanno_object <- make_reanno(output, PAC=pac, mis_fasta_check = TRUE)

## Accessing content and S4/S3 conversion:
names(reanno_object)
overview(reanno_object)
full(reanno_object)
rownames(reanno_object)
length(reanno_object)
nrow(reanno_object)
reanno_s3 <- as(reanno_object, "list")
reanno_s4 <- as.reanno(reanno_s3)

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