scores: Score Calculation from Guidance Objects

In FranzKrah/rGUIDANCE: rGUIDANCE – alignment confidence score computation in R

Score Calculation from Guidance Objects

Description

Calculate scores based on residue pair score inferred by HoT, guidance and guidance2

Usage

scores(guidanceX, score = c("alignment", "column", "residue", "sequence",
  "column_raxml"), na.rm = TRUE, na.raxml = 10, flag_a = FALSE)

Arguments

guidanceX	object of class, see guidance
score	A character string indicating a type of score, currently available are "column", "residue", "alignment", "sequence", "all", or "column_raxml"
na.rm	Logical, indicating if NAs should be removed. If "column_raxml" is used, then this should be FALSE
na.raxml	Integer, specifying what should be used if column score is NA, default is 10 (see Details).
flag_a	character specifying a path. If path is supplied function writes the MSA into a fasta file. Additionally the function produces a file with the column score ready for RAxML input (flag -a) outside of R

Details

The score 'column' is the GUIDANCE column score which is the mean of the residue pair residue score across columns. The score 'alignment' is the mean across the residue pair residue scores. The score 'sequence' is the mean of the residue pair score across rows (sequences). The score 'residue' is the mean score across the residue pairs with that residue (residue pair score).

The GUIDANCE column score can be utilized to weight characters in RAxML (flag -a). Simple removal of sites from the MSA should be done with cautions (Tan et al. 2015). Using score = "column_raxml" allows to use the output directly for ips::raxml (see Vignette for a detailed example). The column score is converted to an integer from 0 to 10. NAs are set to 10 per default, but the user may choose otherwise.

Value

data.frame or list of data.frames with scores

Author(s)

Franz-Sebastian Krah

References

Penn et al. (2010). An alignment confidence score capturing robustness to guide tree uncertainty. Molecular Biology and Evolution 27:1759–1767.

Tan et al. (2015). Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Systematic Biology 64:778–791.

See Also

weights in raxml

FranzKrah/rGUIDANCE documentation built on Jan. 27, 2024, 10:42 a.m.