PBMDesign: Create a new PBMDesign object

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

Description

Create a new PBMDesign object of protein binding microarray probe design information. Alternatively, the function can be called on a PBMExperiment to extract the probe design information associated with experimental data.

Usage

PBMDesign(object, ...)

## S4 method for signature 'data.frame'
PBMDesign(object, ...)

## S4 method for signature 'DataFrame'
PBMDesign(object, ...)

## S4 method for signature 'PBMExperiment'
PBMDesign(object)

Arguments

object	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. Alternatively, a PBMExperiment object to return the associated PBMDesign object.
...	optional probe design parameters to be defined as part of the PBMDesign object. See the PBMDesign class definition for a list of probe design parameters. Important parameters are as described in the Details section below.

Details

Probe design parameters can be specified by name. The following are a couple important parameters which are defined by default for universal PBM designs in the upbmAux package.

1. probeFilter: 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.

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

Value

PBMDesign object.

Author(s)

Patrick Kimes

References

• Berger, M. F., & Bulyk, M. L. (2017). Universal Protein Binding Microarray (PBM) Analysis Suite Homepage. Retrieved October 16, 2020, from http://thebrain.bwh.harvard.edu/PBMAnalysisSuite/indexSep2017.html

See Also

PBMDesign-class

Examples

## Universal array designs included with the Universal PBM Analysis Suite software
## available at the referenced link can be read in as data frames or tibbles (here
## as an object 'mydesign') and converted to a PBMDesign object.
## The 'probeFilter=' and 'probeTrim=' settings here filter to de Bruijn sequences
## and use only the first 36 bases of each probe sequence for downstream analysis.
## Not run: 
PBMDesign(
    object = mydesign, 
    probeFilter = list(probeID = function(x) { grepl("^dBr", x) }), 
    probeTrim = c(1, 36)
)

## End(Not run)

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