annotate_fluorescence_matrix: Annotate fluorescence matrix

In pamelaglopez/hTF_array: Analysis of CoRec and hTF Array Data

Description

Adds probe information to a data frame of fluorescence values. See 'Details' for a description of the inputs, including required annotation columns.

Usage

annotate_fluorescence_matrix(fluorescence_matrix, annotation)

Arguments

fluorescence_matrix	A data frame of fluorescence values, such as output by read_fluorescence_matrices().
annotation	A data frame of PBM probe annotations. See 'Details' for expected columns.

Details

The input fluorescence matrix is expected to be of the form output by read_fluorescence_matrices(), with rows corresponding to probes and columns corresponding to PBM conditions. See read_fluorescence_matrices for a more detailed description of the expected format.

The input annotation table must contain the columns probeID, probe_or, probe_repl, probe_type, ... The expected content of these columns is described in detail below.

probeID

The probe ID. This column will be used to map the probe annotations to the values in the fluorescence matrix, so the IDs in this column must match the IDs in the probeID column in the fluorescence matrix. IDs that are not present in both will be dropped.

probe_or

The orientation of the probe relative to the slide. This column should contain the values "o1" and "o2". Only "o1" rows will be used.

probe_repl

The replicate number of the probe. This column should contain the values "r1", "r2", etc. Only "r1" rows will be used.

probe_type

The probe type. This column should contain the values "MOTIF" and "BACKGROUND".

Value

A data frame of fluorescence values and annotations for each probe.

Examples

annotated_fluorescence_matrix <- annotate_fluorescence_matrix(
    fluorescence_matrix,
    annotation
)

pamelaglopez/hTF_array documentation built on Feb. 23, 2022, 12:05 a.m.