cdsdir2orthofinder: cdsdir2orthofinder

In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R

cdsdir2orthofinder

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs for all possible comparison including self comparison from a directory of CDS fasta files. Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021).

Usage

cdsdir2orthofinder(
  dir,
  file_ending = "*",
  searchtool = "last",
  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1595/bin/"),
  lastD = 1e+06,
  lastm = 10,
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  dbpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  threads = 1,
  remove = FALSE,
  remove.db = FALSE
)

Arguments

dir	directory containing CDS fasta files [mandatory]
file_ending	define file ending to consider [default: *]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1595/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
dbpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
threads	number of parallel threads [default: 1]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]

Value

List of three (crbh=FALSE)

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

aafile2rbh

Examples

## compile last-1542 within CRBHits
CRBHits::make_last()

kullrich/CRBHits documentation built on Nov. 13, 2024, 7:44 a.m.