synder_classes: Synder classes

In arendsee/synder: Use Synteny to Filter Genomic Search

Description

Synder uses the input classes Synmap, GFF and Seqinfo (the last of which is from bioconductor); and the output classes SearchResult and DumpResult.

Details

Each of these classes can be converted from a data.frame with as_* and to a data.frame with as.data.frame.

Synteny maps and the Synmap object

As a data.frame, a synteny map must have the following columns:

1. qseqid - query contig id (e.g. Chr1)

2. qstart - query interval start

3. qstop - query interval stop

4. sseqid - target contig id

5. sstart - target interval start

6. sstop - target interval stop

7. score - score of the syntenic match*

8. strand - relative orientation

score can be any numeric value, it will be transformed as specified by the -x option

It can be from a file with the, where it is required to be TAB-delimited with no header.

The target and query genome lengths files must be TAB-delimited with columns: <name>, <length>

The as_synmap function converts such a data.frame to a Synmap object. A Synmap object is a GRangePairs object (from the bioconductor CNEr package) with socre and strand as meta-columns.

GFF files and the GFF object

GFF files are used to represent queries that will be mapped against the synteny map. These can be loaded into GFF objects with read_gff or converted from data.frames with as_gff. Either way, the resul is a GRange object with source, type, score, phase, and attr meta-columns.

Contig length files and Seqinfo objects

Properly handling boundary cases when mapping requires knowing the length of each contig. This information is provided by the biodonductor Seqinfo objects. The most important information these objects hold is the name and length of all contigs in the assembly. This data can be stored in a two-column data.frame (or headerless, TAB-delimited file).

SearchResult

Holds the results of a successful search run. The class inherits from GRangePairs.

DumpResult

Holds the results of the dump command. The class inherits from GRangePairs.

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