read_agvgdweb_results {agvgd} | R Documentation |
Read in AGVGD Web Results
Description
This function imports into R the results generated by the AGVGD Web application http://agvgd.hci.utah.edu/.
Usage
read_agvgdweb_results(file = stop("`file` is missing"), alignment = NULL)
Arguments
file |
A file path to the results output by the AGVGD Web app. |
alignment |
A character matrix or an alignment object obtained with
|
Value
A tibble of seven columns:
- res
Position of the amino acid residue in the reference protein (first sequence in the alignment). This position corresponds to
poi
minus the gaps in the alignment.- poi
Position of interest, i.e. the alignment position at which the amino acid substitution is being assessed. Because this information is not provided by AGVGD Web app this column is always
NA
; we keep it though for coherence with the output ofagvgd()
.- ref
Reference amino acid, i.e. the amino acid in the first sequence of the alignment, at the position of interest.
- sub
Amino acid substitution being assessed.
- gv
Grantham variation score.
- gd
Grantham difference score.
- prediction
Predicted effect of the amino acid substitution. This is classed as C0, C15, C25, C35, C45, C55, or C65, with C65 most likely to interfere with function and C0 least likely.