pqsfinder {pqsfinder} | R Documentation

## Identify potential quadruplex forming sequences.

### Description

Function for identification of all potential intramolecular quadruplex patterns (PQS) in DNA or RNA sequence.

### Usage

    pqsfinder(subject, strand = "*", overlapping = FALSE, max_len = 50L,
      min_score = 47L, 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, deep = FALSE, verbose = FALSE)

### Arguments

`subject` | DNAString or RNAString 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. The default value 52 shows the best balanced accuracy on G4 sequencing data provided by Chambers et al. 2015.
`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 (`max_bulges + max_mismatches`).
`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: `subject` - Input DNAString or RNAString object, `score` - implicit PQS score, `start` - PQS start position, `width` - PQS width, `loop_1` - start pos. of loop #1, `run_2` - start pos. of run #2, `loop_2` - start pos. of loop #2, `run_3` - start pos. of run #3, `loop_3` - start pos. of loop #3, `run_4` - start pos. of run #4. Return value of the function has to be new score represented as a single integer value. Please note that if `use_default_scoring` is enabled, the custom scoring function is evaluated AFTER the default scoring system but ONLY IF the default scoring system resulted in non-zero score (for performance reasons). On the other hand, when `use_default_scoring` is disabled, custom scoring function is evaluated on every PQS.
`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.
`deep` | Perform deep search. With this option enabled, `maxScores` and `density` vectors are computed. Deep search is much more computationaly demanding.
`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: `start cnt pqs_sequence score`, where `start` is the PQS starting position, `pqs_sequence` shows the PQS sequence structure with each run surrounded by square brackets and `score` is the score assigned to the particular PQS by all applied scoring functions.

### Details

Use `elementMetadata` function to get extra PQS features like number of tetrads (nt), bulges (nb), mismatches (nm) or loop lengths (ll1, ll2, ll3).

### Value

`PQSViews` object

### Examples

    pv <- pqsfinder(DNAString("CCCCCCGGGTGGGTGGGTGGGTAAAA"))
    pv
    elementMetadata(pv)

[Package pqsfinder version 2.2.0 Index]