View source: R/fetch_alphafold_aligned_error.R
fetch_alphafold_aligned_error | R Documentation |
Fetches the aligned error for AlphaFold predictions for provided proteins. The aligned error is useful for assessing inter-domain accuracy. In detail it represents the expected position error at residue x (scored residue), when the predicted and true structures are aligned on residue y (aligned residue).
fetch_alphafold_aligned_error( uniprot_ids = NULL, error_cutoff = 20, timeout = 3600, return_data_frame = FALSE, show_progress = TRUE )
uniprot_ids |
a character vector of UniProt identifiers for which predictions should be fetched. |
error_cutoff |
a numeric value specifying the maximum position error (in Angstroms) that should be retained. setting this value to a low number reduces the size of the retrieved data. Default is 20. |
timeout |
a numeric value specifying the time in seconds until the download of an organism archive times out. The default is 3600 seconds. |
return_data_frame |
a logical value; if |
show_progress |
a logical value; if |
A list that contains aligned errors for AlphaFold predictions. If return_data_frame is TRUE, a data frame with this information is returned instead. The data frame contains the following columns:
scored_residue: The error for this position is calculated based on the alignment to the aligned residue.
aligned_residue: The residue that is aligned for the calculation of the error of the scored residue
error: The predicted aligned error computed by alpha fold.
accession: The UniProt protein identifier.
aligned_error <- fetch_alphafold_aligned_error( uniprot_ids = c("F4HVG8", "O15552"), error_cutoff = 5, return_data_frame = TRUE ) head(aligned_error, n = 10)
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