query_genespace: Query GENESPACE results

In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

Query GENESPACE results

Description

query_genespace Functions to pull data stored in the /pangenome and /syntenicHits directories

query_hits extract syntenic (or all) hits that fall within a interval in a genome.

query_pangenes the primary engine to explore genespace output, this lets you reformat the pan-genes to wide (entry - by - genome) matrix and only look at specified positional bounds.

query_cnv the primary engine to explore genespace output, this lets you reformat the pan-genes to wide (entry - by - genome) matrix and only look at specified positional bounds.

Usage

query_hits(gsParam, bed, synOnly = TRUE)

query_pangenes(
  gsParam,
  bed = NULL,
  refGenome = NULL,
  transform = TRUE,
  showArrayMem = TRUE,
  showNSOrtho = TRUE,
  maxMem2Show = Inf,
  showUnPlacedPgs = FALSE
)

query_cnv(gsParam, bed = NULL, onlyArrayReps = FALSE, maxCopyNumber = Inf)

Arguments

gsParam	A list of genespace parameters created by init_genespace.
bed	A data.table similar to the format of a bed file. At least two columns must be specified: genome, chr. These must match genome-chromosome combinations in the data. The user can also supply two additional columns: start, end. These are the base-pair start and end coordinates of each region. If start and end are not specified, they are set to 0 and Inf respectively so that the entire chromosome is returned.
synOnly	logical, given to query hits to return (or not) the synteny- constrained hits only
refGenome	character matching one of the genomeIDs if a bed object is not provided
transform	logical, should the pangenome be transformed from the long to the wide format?
showArrayMem	logical, should all genes or only the array representative genes (if FALSE) be shown?
showNSOrtho	logical, should non-syntenic orthologs be included in the output?
maxMem2Show	integer specifying the maximum number of members to be included in each entry-by-flag-by-genome combination.
showUnPlacedPgs	logical, when queried should un-located orthogroups be shown?
onlyArrayReps	logical, should only array representatives be considered for CNV counts?
maxCopyNumber	numeric, maximum copyNumber to tabulate. Orthogroups with more than this number are combined into the largest CNV category

Value

a list of data.tables named $genome, $chr: $start-$end. One data.table for each line in the bed file.

jtlovell/GENESPACE documentation built on Jan. 25, 2025, 6:39 a.m.