ExtractBy: Extract and organize 'DNAStringSets's.
In npcooley/SynExtend: Tools for Working With Synteny Objects

ExtractBy

R Documentation

Extract and organize `DNAStringSets`s.

Description

Return organized DNAStringSets based on three currently supported object combinations. First return a single DNAStringSet of feature sequences from a DFrame of genecalls and a DNAStingSet of the source assembly. Second return a list of DNAStringSets of predicted pairs from a PairSummaries object and a character string of the location of a DECIPHER SQLite database. Third return a list of DNAStringSets of predicted single linkage communities from a PairSummaries object, a character string of the location of a DECIPHER SQLite database, and a list of identifiers generated by DisjointSet.

Usage

ExtractBy(x,
          y,
          z,
          Verbose = FALSE)

Arguments

`x`	A `PairSummaries` object, or if `y` is a `DNAStringSet`, a `DFrame` of gene calls such as one generated by `gffToDataFrame`.
`y`	A character vector of length 1 indicating the location of a `DECIPHER` SQLite database. Or, if `x` is a `DFrame`, a `DNAStringSet` of the assembly the gene calls are called from.
`z`	Optional; a list of identifiers generated by `DisjointSet`. Or any list built along a similar format with identifiers paired to the PairSummaries object.
`Verbose`	Logical indicating whether to print progress bars and messages. Defaults to `FALSE`.

Details

All sequences are forced into the same direction based on the Strand column supplied by either the gene calls DFrame specified by x, or the GeneCalls attribute of the PairSummaries object specified by y.

Value

Return a DNAStringSet, or list of DNAStringSets arranged depending upon the objects supplied. See description.

Author(s)

Nicholas Cooley npc19@pitt.edu

Examples

DBPATH <- system.file("extdata",
                      "Endosymbionts_v02.sqlite",
                      package = "SynExtend")
data("Endosymbionts_Pairs03", package = "SynExtend")
data("Endosymbionts_Sets", package = "SynExtend")

# extract the first 10 disjoint sets
Sets <- ExtractBy(x = Endosymbionts_Pairs03,
                  y = DBPATH,
                  z = Endosymbionts_Sets[1:10],
                  Verbose = TRUE)
                  


# extract just the pairs
Sets <- ExtractBy(x = Endosymbionts_Pairs03,
                  y = DBPATH,
                  Verbose = TRUE)

npcooley/SynExtend documentation built on Dec. 20, 2024, 4:03 p.m.