findMapORFs: Find ORFs and immediately map them to their genomic...

In JokingHero/ORFik: Open Reading Frames in Genomics

Find ORFs and immediately map them to their genomic positions.

Description

This function can map spliced ORFs. It finds ORFs on the sequences of interest, but returns relative positions to the positions of 'grl' argument. For example, 'grl' can be exons of known transcripts (with genomic coordinates), and 'seq' sequences of those transcripts, in that case, this function will return genomic coordinates of ORFs found on transcript sequences.

Usage

findMapORFs(
  grl,
  seqs,
  startCodon = startDefinition(1),
  stopCodon = stopDefinition(1),
  longestORF = TRUE,
  minimumLength = 0,
  groupByTx = FALSE,
  grl_is_sorted = FALSE
)

Arguments

grl	A GRangesList of the original sequences that gave the orfs in Genomic coordinates. If grl_is_sorted = TRUE (default), negative exon ranges per grl object must be sorted in descending orders.
seqs	(DNAStringSet or character vector) - DNA/RNA sequences to search for Open Reading Frames. Can be both uppercase or lowercase. Easiest call to get seqs if you want only regions from a fasta/fasta index pair is: seqs = ORFik:::txSeqsFromFa(grl, faFile), where grl is a GRanges/List of search regions and faFile is a FaFile. Note: Remember that if you extracted through a GRanges object, that must have been sorted with negative strand exons descending.
startCodon	(character vector) Possible START codons to search for. Check startDefinition for helper function. Note that it is case sensitive, so "atg" would give 0 hits for a sequence with only capital "ATG" ORFs.
stopCodon	(character vector) Possible STOP codons to search for. Check stopDefinition for helper function. Note that it is case sensitive, so "tga" would give 0 hits for a sequence with only capital "TGA" ORFs.
longestORF	(logical) Default TRUE. Keep only the longest ORF per unique stopcodon: (seqname, strand, stopcodon) combination, Note: Not longest per transcript! You can also use function longestORFs after creation of ORFs for same result.
minimumLength	(integer) Default is 0. Which is START + STOP = 6 bp. Minimum length of ORF, without counting 3bps for START and STOP codons. For example minimumLength = 8 will result in size of ORFs to be at least START + 8*3 (bp) + STOP = 30 bases. Use this param to restrict search.
groupByTx	logical (default: FALSE), should output GRangesList be grouped by exons per ORF (TRUE) or by orfs per transcript (FALSE)?
grl_is_sorted	logical, default FALSE If FALSE will sort negative transcript in descending order for you. If you loaded ranges with default methods this is already the case, so you can set to TRUE to save some time.

Details

This function assumes that 'seq' is in widths relative to 'grl', and that their orders match. 1st seq is 1st grl object, etc.

See vignette for real life example.

Value

A GRangesList of ORFs.

See Also

Other findORFs: findORFs(), findORFsFasta(), findUORFs(), startDefinition(), stopDefinition()

Examples

# First show simple example using findORFs
# This sequence has ORFs at 1-9 and 4-9
seqs <- DNAStringSet("ATGATGTAA") # the dna transcript sequence
findORFs(seqs)
# lets assume that this sequence comes from two exons as follows
# Then we need to use findMapORFs instead of findORFs,
#  for splicing information
gr <- GRanges(seqnames = "1", # chromosome 1
              ranges = IRanges(start = c(21, 10), end = c(23, 15)),
              strand = "-", #
              names = "tx1") #From transcript 1 on chr 1
grl <- GRangesList(tx1 = gr) # 1 transcript with 2 exons
findMapORFs(grl, seqs) # ORFs are properly mapped to its genomic coordinates

grl <- c(grl, grl)
names(grl) <- c("tx1", "tx2")
findMapORFs(grl, c(seqs, seqs))
# More advanced example and how to save sequences found in vignette

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.