cmsearch | R Documentation |
This function calls "cmsearch
" from
Infernal. Infernal must be installed.
The function is focused on
retrieving the hits table and, optionally, producing an alignment.
cmsearch( cm, seq, glocal = TRUE, Z = NULL, output = NULL, alignment = NULL, acc = FALSE, noali = TRUE, notextw = FALSE, textw = NULL, verbose = FALSE, E = NULL, t = NULL, incE = NULL, incT = NULL, cut_ga = FALSE, cut_nc = FALSE, cut_tc = FALSE, filter_strategy = NULL, FZ = NULL, Fmid = NULL, notrunc = FALSE, anytrunc = FALSE, nonull3 = FALSE, mxsize = NULL, smxsize = NULL, cyk = FALSE, acyk = FALSE, wcx = NULL, toponly = TRUE, bottomonly = FALSE, tformat = NULL, cpu = NULL, stall = FALSE, mpi = FALSE, quiet = TRUE )
cm |
(character of length 1) Path to the covariance model (.cm) file.
The covariance model must include calibration data from running
" |
seq |
(filename, character vector,
|
glocal |
( |
Z |
( |
output |
( |
alignment |
( |
acc |
( |
noali |
( |
notextw |
( |
textw |
( |
verbose |
( |
E |
( |
t |
( |
incE |
( |
incT |
( |
cut_ga |
( |
cut_nc |
( |
cut_tc |
( |
filter_strategy |
( |
FZ |
( |
Fmid |
( |
notrunc |
( |
anytrunc |
( |
nonull3 |
( |
mxsize |
( |
smxsize |
( |
cyk |
( |
acyk |
( |
wcx |
( |
toponly |
( |
bottomonly |
( |
tformat |
( |
cpu |
( |
stall |
( |
mpi |
( |
quiet |
( |
a base::data.frame
with columns:
target_name (character) the name of the target sequence
taget_accession(character) the target's accession number
query_name(character) the name of the query CM
query_accession(character) the query CM's accession number
mdl(character) the model type ("cm" or "hmm")
mdl_from(integer) the start location of the hit in the model
mdl_to(integer) the end location of the hit in the model
seq_from(integer) the start location of the hit in the sequence
seq_to(integer) the end location of the hit in the sequence
strand(character) the strand the hit was found on ("+" or "-")
trunc)(character) whether the hit is truncated, and where ("no", "5'", "3'", "5'&3'", or "-" for hmm hits).
pass(integer) which algorithm pass the hit was found on.
gc(numeric) GC content of the hit
bias(numeric) biased composition correction. See the Infernal documentation.
score(numeric) bit-score of the hit, including the biased composition correction.
E_value(numeric) Expectation value for the hit.
inc |
(character) "!" if the sequence meets the inclusion threshold, "?" if it only meets the reporting threshold. |
# search sequences from a fasta file for Rfam RF00002 (5.8S rRNA) cm <- cm_5_8S() sampfasta <- sample_rRNA_fasta() cmsearch(cm = cm, seq = sampfasta, cpu = 1) # also works if the fasta file has already been loaded samp <- Biostrings::readDNAStringSet(sampfasta) cmsearch(cm = cm, seq = samp, cpu = 1)
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