1. MSA2dist
  2. NAMESPACE
Browse code

# MSA2dist 1.11.1 (2024-11-14)

BUG FIXES

* fixed pal2nal
* fixed aastring2aabin to return alignment

NEW FEATURES

* added globalDeletionAA

Kristian Ullrich authored on 14/11/2024 07:08:34
Showing 1 changed files
NAMESPACE
History View file @ b5ab038
... ... 
@@ -29,6 +29,7 @@ export(dnastring2kaks)
29 29 
 export(getmask)
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 export(getpos)
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 export(globalDeletion)
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+export(globalDeletionAA)
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 export(granthamMatrix)
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 export(indices2kaks)
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 export(iupacMatrix)
... ... 
@@ -46,6 +47,7 @@ export(string2region)
46 47 
 export(subString)
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 export(uptriidx)
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 import(Rcpp)
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+importFrom(Biostrings,AAMultipleAlignment)
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 importFrom(Biostrings,AAString)
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 importFrom(Biostrings,AAStringSet)
51 53 
 importFrom(Biostrings,BString)
Browse code

pairwiseAlignment() has moved from Biostrings to pwalign

Hervé Pagès authored on 24/04/2024 01:45:02
Showing 1 changed files
NAMESPACE
History View file @ dbfa534
... ... 
@@ -58,7 +58,6 @@ importFrom(Biostrings,RNAString)
58 58 
 importFrom(Biostrings,RNAStringSet)
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 importFrom(Biostrings,consensusMatrix)
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 importFrom(Biostrings,getGeneticCode)
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-importFrom(Biostrings,pairwiseAlignment)
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 importFrom(Biostrings,readAAStringSet)
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 importFrom(Biostrings,readDNAStringSet)
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 importFrom(Biostrings,subseq)
... ... 
@@ -78,19 +77,13 @@ importFrom(ape,as.AAbin)
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 importFrom(ape,as.DNAbin.alignment)
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 importFrom(ape,dist.dna)
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 importFrom(doParallel,registerDoParallel)
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-importFrom(dplyr,arrange)
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 importFrom(dplyr,count)
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-importFrom(dplyr,desc)
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-importFrom(dplyr,distinct)
85 81 
 importFrom(dplyr,filter)
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 importFrom(dplyr,group_by)
87 83 
 importFrom(dplyr,left_join)
88 84 
 importFrom(dplyr,mutate)
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-importFrom(dplyr,reframe)
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-importFrom(dplyr,select)
91 85 
 importFrom(dplyr,slice)
92 86 
 importFrom(dplyr,summarise)
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-importFrom(dplyr,ungroup)
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 importFrom(foreach,"%do%")
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 importFrom(foreach,"%dopar%")
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 importFrom(foreach,foreach)
... ... 
@@ -98,12 +91,12 @@ importFrom(methods,is)
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 importFrom(methods,slot)
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 importFrom(parallel,makeForkCluster)
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 importFrom(parallel,stopCluster)
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+importFrom(pwalign,pairwiseAlignment)
101 95 
 importFrom(rlang,.data)
102 96 
 importFrom(seqinr,as.alignment)
103 97 
 importFrom(seqinr,kaks)
104 98 
 importFrom(stats,setNames)
105 99 
 importFrom(stringr,str_split)
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-importFrom(stringr,str_split_fixed)
107 100 
 importFrom(stringr,str_sub)
108 101 
 importFrom(stringr,word)
109 102 
 importFrom(tibble,add_column)
Browse code

# update to version 1.7.1

Kristian Ullrich authored on 13/03/2024 16:56:18
Showing 1 changed files
NAMESPACE
History View file @ 290ae43
... ... 
@@ -14,6 +14,7 @@ export(aln2aastring)
14 14 
 export(aln2dnastring)
15 15 
 export(cds2aa)
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 export(cds2codonaln)
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+export(cdsstring2codonaln)
17 18 
 export(codon2numberAMBIG)
18 19 
 export(codon2numberTCAG)
19 20 
 export(codonmat2pnps)
... ... 
@@ -29,8 +30,10 @@ export(getmask)
29 30 
 export(getpos)
30 31 
 export(globalDeletion)
31 32 
 export(granthamMatrix)
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+export(indices2kaks)
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 export(iupacMatrix)
33 35 
 export(makePostalignedSeqs)
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+export(pal2nal)
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 export(popinteger)
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 export(popnames)
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 export(rcpp_KaKs)
... ... 
@@ -75,13 +78,19 @@ importFrom(ape,as.AAbin)
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 importFrom(ape,as.DNAbin.alignment)
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 importFrom(ape,dist.dna)
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 importFrom(doParallel,registerDoParallel)
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+importFrom(dplyr,arrange)
78 82 
 importFrom(dplyr,count)
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+importFrom(dplyr,desc)
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+importFrom(dplyr,distinct)
79 85 
 importFrom(dplyr,filter)
80 86 
 importFrom(dplyr,group_by)
81 87 
 importFrom(dplyr,left_join)
82 88 
 importFrom(dplyr,mutate)
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+importFrom(dplyr,reframe)
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+importFrom(dplyr,select)
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 importFrom(dplyr,slice)
84 92 
 importFrom(dplyr,summarise)
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+importFrom(dplyr,ungroup)
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 importFrom(foreach,"%do%")
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 importFrom(foreach,"%dopar%")
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 importFrom(foreach,foreach)
... ... 
@@ -94,6 +103,7 @@ importFrom(seqinr,as.alignment)
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 importFrom(seqinr,kaks)
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 importFrom(stats,setNames)
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 importFrom(stringr,str_split)
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+importFrom(stringr,str_split_fixed)
97 107 
 importFrom(stringr,str_sub)
98 108 
 importFrom(stringr,word)
99 109 
 importFrom(tibble,add_column)
Browse code

# added aa2selfscore

Kristian Ullrich authored on 24/05/2023 18:31:50
Showing 1 changed files
NAMESPACE
History View file @ a1139a4
... ... 
@@ -1,6 +1,7 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 3 
 export(GENETIC_CODE_TCAG)
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+export(aa2selfscore)
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 export(aabin2aastring)
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 export(aastring2aabin)
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 export(aastring2aln)
... ... 
@@ -101,4 +102,5 @@ importFrom(tidyr,"%>%")
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 importFrom(tidyr,as_tibble)
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 importFrom(tidyr,pivot_longer)
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 importFrom(tidyr,unite)
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+importFrom(utils,data)
104 106 
 useDynLib(MSA2dist, .registration = TRUE)
Browse code

#changed rcpp_KaKs return type into list

Kristian Ullrich authored on 19/09/2022 15:07:05
Showing 1 changed files
NAMESPACE
History View file @ 174cb1f
... ... 
@@ -92,6 +92,7 @@ importFrom(rlang,.data)
92 92 
 importFrom(seqinr,as.alignment)
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 importFrom(seqinr,kaks)
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 importFrom(stats,setNames)
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+importFrom(stringr,str_split)
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 importFrom(stringr,str_sub)
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 importFrom(stringr,word)
97 98 
 importFrom(tibble,add_column)
Browse code

#port of KaKs Calculator 2.0 with Rcpp into MSA2dist #added new codon models to test-dnastring2kaks #changed version #added new codon models references

Kristian Ullrich authored on 06/07/2022 08:49:06
Showing 1 changed files
NAMESPACE
History View file @ a9a46d6
... ... 
@@ -32,6 +32,7 @@ export(iupacMatrix)
32 32 
 export(makePostalignedSeqs)
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 export(popinteger)
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 export(popnames)
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+export(rcpp_KaKs)
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 export(rcpp_distSTRING)
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 export(rcpp_pairwiseDeletionAA)
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 export(rcpp_pairwiseDeletionDNA)
... ... 
@@ -94,6 +95,7 @@ importFrom(stats,setNames)
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 importFrom(stringr,str_sub)
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 importFrom(stringr,word)
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 importFrom(tibble,add_column)
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+importFrom(tibble,column_to_rownames)
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 importFrom(tidyr,"%>%")
98 100 
 importFrom(tidyr,as_tibble)
99 101 
 importFrom(tidyr,pivot_longer)
Browse code

#added cds2codonaln

Kristian Ullrich authored on 30/06/2022 12:17:50
Showing 1 changed files
NAMESPACE
History View file @ 4d5aedd
... ... 
@@ -12,6 +12,7 @@ export(addregion2string)
12 12 
 export(aln2aastring)
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 export(aln2dnastring)
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 export(cds2aa)
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+export(cds2codonaln)
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 export(codon2numberAMBIG)
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 export(codon2numberTCAG)
17 18 
 export(codonmat2pnps)
... ... 
@@ -28,6 +29,7 @@ export(getpos)
28 29 
 export(globalDeletion)
29 30 
 export(granthamMatrix)
30 31 
 export(iupacMatrix)
32 
+export(makePostalignedSeqs)
31 33 
 export(popinteger)
32 34 
 export(popnames)
33 35 
 export(rcpp_distSTRING)
Browse code

#fix RcppThread::LdFlags warning

Kristian Ullrich authored on 18/03/2022 08:19:24
Showing 1 changed files
NAMESPACE
History View file @ 42d3c4f
... ... 
@@ -39,7 +39,6 @@ export(string2region)
39 39 
 export(subString)
40 40 
 export(uptriidx)
41 41 
 import(Rcpp)
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-import(RcppThread)
43 42 
 importFrom(Biostrings,AAString)
44 43 
 importFrom(Biostrings,AAStringSet)
45 44 
 importFrom(Biostrings,BString)
Browse code

#changed name from distSTRING to MSA2dist #added accessors

Kristian Ullrich authored on 22/12/2021 23:24:09
Showing 1 changed files
NAMESPACE
History View file @ 6a3ff30
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,100 @@
1 
+# Generated by roxygen2: do not edit by hand
2 
+
3 
+export(GENETIC_CODE_TCAG)
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+export(aabin2aastring)
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+export(aastring2aabin)
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+export(aastring2aln)
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+export(aastring2dist)
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+export(addmask2string)
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+export(addpop2string)
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+export(addpos2string)
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+export(addregion2string)
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+export(aln2aastring)
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+export(aln2dnastring)
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+export(cds2aa)
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+export(codon2numberAMBIG)
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+export(codon2numberTCAG)
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+export(codonmat2pnps)
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+export(codonmat2xy)
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+export(compareCodons)
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+export(dnabin2dnastring)
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+export(dnastring2aln)
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+export(dnastring2codonmat)
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+export(dnastring2dist)
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+export(dnastring2dnabin)
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+export(dnastring2kaks)
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+export(getmask)
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+export(getpos)
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+export(globalDeletion)
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+export(granthamMatrix)
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+export(iupacMatrix)
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+export(popinteger)
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+export(popnames)
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+export(rcpp_distSTRING)
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+export(rcpp_pairwiseDeletionAA)
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+export(rcpp_pairwiseDeletionDNA)
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+export(region)
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+export(regionused)
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+export(string2region)
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+export(subString)
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+export(uptriidx)
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+import(Rcpp)
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+import(RcppThread)
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+importFrom(Biostrings,AAString)
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+importFrom(Biostrings,AAStringSet)
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+importFrom(Biostrings,BString)
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+importFrom(Biostrings,BStringSet)
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+importFrom(Biostrings,DNAString)
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+importFrom(Biostrings,DNAStringSet)
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+importFrom(Biostrings,GENETIC_CODE)
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+importFrom(Biostrings,GENETIC_CODE_TABLE)
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+importFrom(Biostrings,RNAString)
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+importFrom(Biostrings,RNAStringSet)
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+importFrom(Biostrings,consensusMatrix)
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+importFrom(Biostrings,getGeneticCode)
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+importFrom(Biostrings,pairwiseAlignment)
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+importFrom(Biostrings,readAAStringSet)
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+importFrom(Biostrings,readDNAStringSet)
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+importFrom(Biostrings,subseq)
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+importFrom(Biostrings,translate)
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+importFrom(Biostrings,width)
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+importFrom(Biostrings,writeXStringSet)
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+importFrom(GenomicRanges,GRanges)
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+importFrom(IRanges,IRanges)
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+importFrom(IRanges,IRangesList)
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+importFrom(IRanges,disjoin)
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+importFrom(IRanges,end)
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+importFrom(IRanges,findOverlaps)
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+importFrom(IRanges,overlapsRanges)
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+importFrom(IRanges,reduce)
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+importFrom(IRanges,start)
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+importFrom(ape,as.AAbin)
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+importFrom(ape,as.DNAbin.alignment)
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+importFrom(ape,dist.dna)
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+importFrom(doParallel,registerDoParallel)
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+importFrom(dplyr,count)
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+importFrom(dplyr,filter)
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+importFrom(dplyr,group_by)
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+importFrom(dplyr,left_join)
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+importFrom(dplyr,mutate)
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+importFrom(dplyr,slice)
81 
+importFrom(dplyr,summarise)
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+importFrom(foreach,"%do%")
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+importFrom(foreach,"%dopar%")
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+importFrom(foreach,foreach)
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+importFrom(methods,is)
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+importFrom(methods,slot)
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+importFrom(parallel,makeForkCluster)
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+importFrom(parallel,stopCluster)
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+importFrom(rlang,.data)
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+importFrom(seqinr,as.alignment)
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+importFrom(seqinr,kaks)
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+importFrom(stats,setNames)
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+importFrom(stringr,str_sub)
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+importFrom(stringr,word)
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+importFrom(tibble,add_column)
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+importFrom(tidyr,"%>%")
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+importFrom(tidyr,as_tibble)
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+importFrom(tidyr,pivot_longer)
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+importFrom(tidyr,unite)
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+useDynLib(MSA2dist, .registration = TRUE)