View source: R/expression_funks.R
interVsIntraSpeciesExpressionProfileDists | R Documentation |
expr.prof.dists
which is expected to be an instance of class
base::dist
(See expressionProfilesDists
for more details).Extracts the inter- and intra-species distances from argument object
expr.prof.dists
which is expected to be an instance of class
base::dist
(See expressionProfilesDists
for more details).
interVsIntraSpeciesExpressionProfileDists(expr.prof.dists,
gene.ids.to.specs.regex = list(ath = "^AT[0-9CM]G\\d+$", chi =
"^CARHR\\d+$"))
expr.prof.dists |
an instance of |
gene.ids.to.specs.regex |
A named character where the names are species
and the values are regular expressions capable of uniquely identifying which
species a gene accession belongs to. Default is |
A list with either data.frame or numeric values. Data.frames have
three columns, two indicating gene pairs and the third the extracted
distances, while numeric values point to maximum distances. Result list
names are the species found as names in gene.ids.to.specs.regex
,
inter.species
, max.inter.species
, and for each species
spec_i
one max.spec_i
.
Validate input:
Initialize:
Validate species:
Extract the requested intra-species distances:
Do not extract meaningless distances for pairs of identical
genes, e.g. (gene_a, gene_a):
Extract the requested inter-species distances:
Return result as list:
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