mapKmers: Map K-mer Motifs to PBM Probe Sequences

In pkimes/upbm: Tools for the analysis of universal protein binding microarrays

Description

This helper function takes a PBMDesign object and set of k-mer sequences of interest, and returns a mapping between probes and k-mer sequences. Since no probe filtering or trimming is performed as part of this function, pbmTrimProbes and pbmFilterProbes should be called before passing the PBMDesign object to this function.

Usage

mapKmers(pd, kmers)

Arguments

pd	a PBMDesign object containing probe sequence information.
kmers	character vector of K-mers (of equal length) to which probes should be mapped.

Value

A table of k-mer sequences and probes, with each row corresponding to an occurrence of a k-mer sequence on a probe. The table inclues all columns of the input pd design as well as columns indicating the orientation (orient) and position (pos) of the k-mer in the probe.

Author(s)

Patrick Kimes

pkimes/upbm documentation built on Oct. 17, 2020, 9:10 a.m.