PBMDesign-class: PBMDesign class

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

Description

Simple class to store array design information for universal protein binding microarray (uPBM) data for use with functions in the upbm package. Array information is comprised of three elements.

Slots

design

a data.frame with each row corresponding to a probe on the array. Must include ‘Sequence’ and (unique) ‘probeID’ columns, along with any other metadata for probes, e.g. array ‘Row’ or ‘Column’ spatial coordinates.

probeFilter

an optional named list of probe filters to be used to subset probes during data analysis steps. List names must correspond to columns in ‘design’. List entries must be single-parameter functions to be called on the corresponding column to return a logical vector of probes to keep (TRUE) and drop (FALSE) during analysis.

probeTrim

an optional integer vector of length 2 specifying start and end positions in probe ‘Sequence’ to use in analysis steps.

Author(s)

Patrick Kimes

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