replace_identified_by_x

Helper function for the calculation of sequence coverage, replaces identified positions with an
"x" within the protein sequence.

Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.

Jan-Philipp Quast

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data
Analysis Tools

Dina Schuster

ETH Zurich 

replace_identified_by_x function

<dl><dt>sequence</dt>
<dd>a character value that contains the protein sequence.</dd>
<dt>positions_start</dt>
<dd>a numeric vector of start positions of the identified peptides.</dd>
<dt>positions_end</dt>
<dd>a numeric vector of end positions of the identified peptides.</dd></dl>

Arguments

Replace identified positions in protein sequence by "x" — replace_identified_by_x

<dl>

<dt>sequence</dt>
<dd>a character value that contains the protein sequence.</dd>


<dt>positions_start</dt>
<dd>a numeric vector of start positions of the identified peptides.</dd>


<dt>positions_end</dt>
<dd>a numeric vector of end positions of the identified peptides.</dd>

</dl>

replace_identified_by_x: Replace identified positions in protein sequence by "x"

Description

Usage

Value

Arguments