PBMExperiment-class: PBMExperiment class

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

Description

Extension of the SummarizedExperiment class to store universal protein binding microarray (uPBM) data for use with functions in the upbm package.

Slots

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 RowData. 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.

probeCols

an optional character vector of rowData column names corresponding to probe design information.

Author(s)

Patrick Kimes

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