read baseml output
read.codeml(rstfile, mlcfile, tree = "mlc", type = "Joint")
Arguments
| rstfile | rst file |
|---|---|
| mlcfile | mlc file |
| tree | one of 'mlc' or 'rst' |
| type | one of 'Marginal' or 'Joint' |
Value
A treedata object
Author
Guangchuang Yu
Examples
rstfile <- system.file("extdata/PAML_Codeml", "rst", package="treeio") mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio") read.codeml(rstfile, mlcfile) #> 'treedata' S4 object that stored information of #> '/usr/local/lib/R/site-library/treeio/extdata/PAML_Codeml/rst', #> '/usr/local/lib/R/site-library/treeio/extdata/PAML_Codeml/mlc'. #> #> [email protected] phylo: #> #> Phylogenetic tree with 15 tips and 13 internal nodes. #> #> Tip labels: #> A, B, C, D, E, F, ... #> Node labels: #> 16, 17, 18, 19, 20, 21, ... #> #> Unrooted; includes branch lengths. #> #> with the following features available: #> 'subs', 'AA_subs', 't', 'N', 'S', 'dN_vs_dS', 'dN', 'dS', 'N_x_dN', 'S_x_dS'. #> #> # The associated data tibble abstraction: 28 × 13 #> # The 'node', 'label' and 'isTip' are from the phylo tree. #> node label isTip subs AA_subs t N S dN_vs_dS dN dS #> <dbl> <chr> <lgl> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 1 A TRUE C214T /… "K603R" 0.01 1515. 633. 0.0646 0.0007 0.0101 #> 2 2 B TRUE C222T /… "" 0.032 1515. 633. 0.0001 0 0.0358 #> 3 3 C TRUE A204G /… "N272S /… 0.028 1515. 633. 0.0461 0.0013 0.0282 #> 4 4 D TRUE A111G /… "K104R /… 0.082 1515. 633. 0.0385 0.0033 0.0849 #> 5 5 E TRUE C174T /… "T208S /… 0.031 1515. 633. 0.0641 0.002 0.0305 #> 6 6 F TRUE T829C /… "S277P /… 0.007 1515. 633. 0.298 0.0013 0.0044 #> 7 7 G TRUE A5T / A… "E2V / A… 0.046 1515. 633. 0.162 0.006 0.0373 #> 8 8 H TRUE A112G /… "I38V / … 0.021 1515. 633. 0.103 0.002 0.0191 #> 9 9 I TRUE T211C /… "" 0.015 1515. 633. 0.0001 0 0.0167 #> 10 10 J TRUE G295A /… "G99R" 0.014 1515. 633. 0.0457 0.0007 0.0143 #> # … with 18 more rows, and 2 more variables: N_x_dN <dbl>, S_x_dS <dbl>