synder_commands: Synder Commands

In arendsee/synder: Use Synteny to Filter Genomic Search

Description

Synder Commands

Usage

search(syn, gff, tcl = "", qcl = "", swap = FALSE, trans = "i",
  k = 0L, r = 0, offsets = c(1L, 1L))

dump(syn, swap = FALSE, trans = "i", k = 0L, r = 0,
  offsets = c(1L, 1L))

Arguments

syn	synteny map file name or object
gff	GFF file of input intervals
tcl	target genome lengths file or object
qcl	query genome lengths file or object
swap	reverse direction of synteny map (target -> query)
trans	synteny map score transform (Synder requires additive scores) i -> f(S) = S (default, no transformation) d -> f(S) = L * S (transform from score densities) p -> f(S) = L * S / 100 (transform from percent identity) l -> f(S) = -log(S) (transform from e-values or p-values) Where S is input score and L interval length
k	Number of interrupting intervals allowed before breaking contiguous set.
r	Score decay rate.
offsets	Start and stop offsets (0 or 1) for the synteny map

Search Command

search predicts search intervals.

This is the primary function of synder. A set of intervals in one genome (the query) is mapped to a set of intervals in another genome (the target). The input intervals may fall between query-side syntenic intervals, in which case, the search interval also will fall inbetween target syntenic intervals.

The output is a table with the following fields:

1. query interval name (e.g. AT1G20300)

2. query chromosome name

3. query start position

4. query stop position

5. target chromosome name

6. search interval start position on target chromsome

7. search interval stop position on target chromsome

8. search interval strand ('+' / '-')

9. score

10. contiguous set id

11. lower flag

    • 0 lower bound is inside a syntenic interval

    • 1 lower bound is between intervals in a contiguous set

    • 2 lower bound does not overlap the contiguous set

    • 3 lower bound is beyond any syntenic interval (near end of scaffold)

12. upper flag - see lower flag

13. inbetween flag - TRUE if the query interval overlaps no syntenic intervals

Dump command

Builds the internal synteny datastructure and prints the results.

For example, given the file

que   100    200    tar   1100   1200   100   +
que   1100   1800   tar   1500   1900   100   +
que   1400   1700   tar   1600   2000   100   +
que   1200   1600   tar   1700   2100   100   +
que   1300   1900   tar   1800   2200   100   +

R> synder::dump('que-tar.syn', trans='p')
que  100   200   tar  1100  1200  101.000000  +  0
que  1100  1900  tar  1500  2200  700.084964  +  0

In the above example, dump shows that blocks 2-5 are merged (since they are doubly-overlapping) and shows the results of the score transformations. It is this dumped synteny map that would have been used in any filter or search operations.

Also note the addition of a 9th column. This column specifies that contiguous set. In this case, all blocks, after merging, are in the same set.

arendsee/synder documentation built on May 10, 2019, 1:26 p.m.