dbReadMSA: Read Sequences from Database
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Value See Also

Reads selected and assembled sequences (see stepF and subsequent steps) from the database, specifically from the table 'sequence_selected'.

dbReadMSA(
  x,
  locus,
  taxon,
  regex = TRUE,
  label = c("taxon", "acc"),
  confid.scores = "all",
  row.confid = 0,
  col.confid = 0,
  ignore.excluded = TRUE,
  blocks = "ignore"
)

`x`	An object of class `megapteraProj`.
`locus`	A vector of mode `"character"` giving a locus name. This argument is optional and, if specified, will override the locus definition in `x`.
`taxon`	A vector of mode `"character"` used to choose a subset of vailable taxa. This can be either one or more taxon names or a regular expression.
`regex`	Logical: if `TRUE`, the string given via `taxon` will be interpreted as a regular expression (see `regex`).
`label`	A vector of mode `"character"` giving the attributes for constructing the sequences labels, e.g. `"taxon"`, `"acc"`, or both.
`confid.scores`	A vector of mode `"character"` specifying if and how confidence scores will be returned. Use `"ignore"` to omit confidence scores. Other options are `"all"`, `"row.means"`, and `"col.means"`. Confidence scores are returned as an attribute and can be accessed by `attr(obj, "cs")`.
`row.confid`	A real number in the interval `[0, 1]` giving the confidence threshold for alignment rows (i.e. taxa, sequences); only rows scoring equal or greater to `min.confid` will be selected.
`col.confid`	A real number in the interval `[0, 1]` giving the confidence threshold for alignment columns (i.e. nucletide positions); only rows (i.e. taxa, sequences) or columns scoring equal or greater to `min.confid` will be selected.
`ignore.excluded`	Currently unused.
`blocks`	Currently unused.