annot_apply_RNA_ptt: Annotation function of the APERO package

In Simon-Leonard/APERO: Analysis of Paired-End RNA-seq Output

Annotation function of the APERO package

Description

RNAs or start regions are classified according to their localization regarding to CDS and strand from which they are transcribed.

Orphan sRNAs are transcribed from intergenic regions.

Transcribed from the same strand of the CDS are: P RNAs/start region corresponding to primary RNAs/start region located in the 250 nucleotides (nt) upstream the CDS without overlapping it; 5'-UTR and 3'-UTR RNAs/start region overlapping start and stop codon respectively.

Transcribed from the opposite strand of the CDS are: Ai corresponding to antisense RNAs/start region transcribed inside CDS; Div corresponding to RNAs/start region starting in the 250 nucleotides (nt) upstream the CDS; 5'Ai and 3'Ai RNAs/start region overlapping start and stop codon respectively.

Usage

annot_apply_RNA_ptt(data,ref,genome_size)

Arguments

data	6 columns data.frame. 1st column = "Position"; 6th column = "Positional.Uncertainty"; One column (2nd, 3rd, 4th or 5th) has to be "str" (for strand)
ref	ptt-like annotation data.frame. Example : Location Strand Length PID Gene Synonym Code COG Product 190..255 + 21 16127995 thrL b0001 - - thr operon leader peptide 337..2799 + 820 16127996 thrA b0002 - COG0527E,COG0527E Bifunctional aspartokinase/homoserine dehydrogenase 1 2801..3733 + 310 16127997 thrB b0003 - COG0083E,COG0083E homoserine kinase 3734..5020 + 428 16127998 thrC b0004 - COG0498E,COG0498E L-threonine synthase
genome_size	Genome size

Value

Returns an 8 columns table : The input data merged with a "Class" column (short annotation) and a "Comment" column (detailed annotation)

Author(s)

Simon Leonard

Simon-Leonard/APERO documentation built on June 17, 2022, 10:31 a.m.