pqsfinder {pqsfinder} | R Documentation |
Function for identification of all potential intramolecular quadruplex patterns (PQS) in DNA sequence.
pqsfinder(subject, strand = "*", overlapping = FALSE, max_len = 50L, min_score = 26L, run_min_len = 2L, run_max_len = 11L, loop_min_len = 0L, loop_max_len = 30L, max_bulges = 3L, max_mismatches = 3L, max_defects = 3L, tetrad_bonus = 40L, mismatch_penalty = 28L, bulge_penalty = 20L, bulge_len_factor = 0.2, bulge_len_exponent = 1, loop_mean_factor = 6.6, loop_mean_exponent = 0.8, run_re = "G{1,10}.{0,9}G{1,10}", custom_scoring_fn = NULL, use_default_scoring = TRUE, verbose = FALSE)
subject |
DNAString object. |
strand |
Strand specification. Allowed values are "+", "-" or "*", where the last one represents both strands. Implicitly, the input DNAString object is assumed to encode the "+" strand. |
overlapping |
If true, than all overlapping PQS will be reported. |
max_len |
Maximal lenth of PQS. |
min_score |
Minimal PQS score. |
run_min_len |
Minimal length of quadruplex run. |
run_max_len |
Maximal length of quadruplex run. |
loop_min_len |
Minimal length of quadruplex loop. Unless the default scoring system is disabled, at most one loop can have zero length. |
loop_max_len |
Maxmimal length of quadruplex loop. |
max_bulges |
Maximal number of runs with bulge. |
max_mismatches |
Maximal number of runs with mismatch. |
max_defects |
Maximum number of defects in total ( |
tetrad_bonus |
Score bonus for one complete G tetrade. |
mismatch_penalty |
Penalization for a mismatch in tetrad. |
bulge_penalty |
Penalization for a bulge in quadruplex run. |
bulge_len_factor |
Penalization factor for a bulge length. |
bulge_len_exponent |
Exponent of bulge length. |
loop_mean_factor |
Penalization factor of loop length mean. |
loop_mean_exponent |
Exponent of loop length mean. |
run_re |
Regular expression specifying one run of quadruplex. |
custom_scoring_fn |
Custom quadruplex scoring function. It takes the
following 10 arguments: |
use_default_scoring |
Enables default internal scoring system. This option is particularly useful in case you intend to radically change the default behavior and specify your own scoring function. By disabling the default scoring you will get a full control above the underlying detection algorithm. |
verbose |
Enables detailed output. Turn it on if you want to see all
possible PQS found at each positions and not just the best one. It is
highly recommended to use this option for debugging custom quadruplex
scoring function. Each PQS is reported on separate row in the following
format: |
Use elementMetadata
function to get extra PQS features
like number of tetrads (nt), bulges (nb), mismatches (nm) or loop lengths
(ll1, ll2, ll3).
PQSViews
object
pv <- pqsfinder(DNAString("CCCCCCGGGTGGGTGGGTGGTAAAA")) pv elementMetadata(pv)