count_substring_fixed

stringi has no function that search within substring without memory copy it.
This function has two versions. One without the need to memory copy denoted
as ***. The only downside to this is std::string::find cannot stop searching
past end of substring. I manage to at least stop it as soon as possible. If
the pattern is long and rare, it won't stop until it find post-substring
pattern. The other version is memory copy substring but as this operation is
in the loop, the memory is still within comfortable range. c++17 has
std::string_view that solve this but still new and not widely available. Use
count_substring_regex to avoid memory copy.

A multi-purpose and flexible k-meric enrichment analysis software.
'kmeRtone' measures the enrichment of k-mers by comparing the population of
k-mers in the case loci with a carefully devised internal negative control
group, consisting of k-mers from regions close to, yet sufficiently distant
from, the case loci to mitigate any potential sequencing bias. This method
effectively captures both the local sequencing variations and broader
sequence influences, while also correcting for potential biases, thereby
ensuring more accurate analysis. The core functionality of 'kmeRtone' is
the SCORE() function, which calculates the susceptibility scores for k-mers in
case and control regions. Case regions are defined by the genomic coordinates
provided in a file by the user and the control regions can be constructed
relative to the case regions or provided directly. The k-meric susceptibility
scores are calculated by using a one-proportion z-statistic. 'kmeRtone' is
highly flexible by allowing users to also specify their target k-mer patterns
and quantify the corresponding k-mer enrichment scores in the context of
these patterns, allowing for a more comprehensive approach to understanding
the functional implications of specific DNA sequences on a genomic scale
(e.g., CT motifs upon UV radiation damage).
Adib A. Abdullah, Patrick Pflughaupt, Claudia Feng, Aleksandr B. Sahakyan (2024) Bioinformatics (submitted).

Aleksandr B. Sahakyan

kmeRtone

Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Adib Abdullah

Patrick Pflughaupt

Aleksandr Sahakyan

count_substring_fixed function

<dl><dt>sequence</dt>
<dd>A sequence to map.</dd>
<dt>start</dt>
<dd>Start positions.</dd>
<dt>end</dt>
<dd>End positions.</dd>
<dt>pattern</dt>
<dd>A pattern to search for.</dd></dl>

Arguments

Count sequence content in a given sequence. — count_substring_fixed

<dl>

<dt>sequence</dt>
<dd>A sequence to map.</dd>


<dt>start</dt>
<dd>Start positions.</dd>


<dt>end</dt>
<dd>End positions.</dd>


<dt>pattern</dt>
<dd>A pattern to search for.</dd>

</dl>

count_substring_fixed: Count sequence content in a given sequence.

Description

Usage

Value

Arguments