full: full(reanno)

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

full(reanno)

Description

Access the multilevel list of imported data.frames in a S4 reanno object

Usage

full(object)

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

## S4 replacement method for signature 'reanno,list'
full(object) <- value

Arguments

object	A S4 reanno-object containing an Full_anno list.
value	List of tibble data.frames with the same property as the Full_anno list of tibble data.frames in 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

All the results that were imported into the reanno-object returned as a list of tibble data.frames (class tbl_df, tbl, data.frame).

Updated S4 reanno-object.

See Also

Other reanno methods: overview()

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.