make_corecmotifs: Make a list of CoRecMotifs

In Siggers-Lab/hTF_array: Process and Visualize CoRec Data

Make a list of CoRecMotifs

Description

Creates a list of CoRecMotifs using fluorescence data from a CoRec experiment. This is a convenience function that calls annotate_fluorescence_table(), fluorescence_to_zscore_table(), and then zscore_table_to_corecmotifs().

Usage

make_corecmotifs(
  fluorescence_table,
  fluorescence_columns,
  annotation,
  array_id = NULL,
  output_directory = NULL,
  output_base_name = NULL
)

Arguments

fluorescence_table	data.frame. A table of fluorescence values.
fluorescence_columns	character. The names of the columns of fluorescence_table that contain fluorescence data.
annotation	data.frame. The probe annotations to add to the fluorescence table. See hTF_v1_annotation for expected annotation columns.
array_id	character(1) or NULL. The name of the array/experiment the z-scores are from. If NULL, a random ID will be generated. (Default: NULL)
output_directory	character(1) or NULL. The path to the directory where output files will be saved. No output files will be created unless output_directory or output_base_name is provided. (Default: NULL)
output_base_name	character(1) or NULL. The base name for output files. No output files will be created unless output_directory or output_base_name is provided. (Default: NULL)

Details

By default no output files are created. To save output files, you must provide output_directory, output_base_name, or both. The output files are named according to the following rules.

• If output_directory is provided but output_base_name is not, the files will be saved in the provided directory using the base name "output".

• If output_base_name is provided but output_directory is not, the files will be saved in the working directory using the provided base name.

• If array_id is provided, it will be appended to the output base name.

• The individual output file names will be identified by a suffix appended to the output base name after the array ID (if present).

• The output of annotate_fluorescence_table() will have the suffix "fluorescence.tsv".

• The output of fluorescence_to_zscore_table() will have the suffix "zscores.tsv"

• The output of zscore_table_to_corecmotifs() will have the suffix "all_corecmotifs.rds"

Value

A list of CoRecMotifs, one for each possible combination of the probe sets annotated in annotation and the PBM conditions listed in pbm_conditions.

See Also

annotate_fluorescence_table(), fluorescence_to_zscore_table(), zscore_table_to_corecmotifs()

Examples

print("FILL THIS IN!")

Siggers-Lab/hTF_array documentation built on Feb. 7, 2024, 11:25 p.m.