load_epik_config: Load and validate configuration file

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Load and validate configuration file

Usage

load_epik_config(config_file, export_env = parent.frame(), validate = NULL)

Arguments

config_file	path of configuration file
export_env	environment where to export variables
validate	whether do validation

Details

To run functions in epic package smoothly, users can validate their data by load_epik_config function. All necessary variables are initialized in a configuration file. The configuration file should provide following variables:

SAMPLE: a data frame, row names must be sample id and there must be a 'class' column which corresponds to classes of samples. There can also be other annotation columns.

COLOR: a list of color settings corresponding to annotation column in 'SAMPLE'. The value of each list element must be either a named vector or a color mapping function. 'COLOR$class' must be defined or random color will be assigned. Names of other color settings should be same as corresponding columns in 'SAMPLE'.

TXDB (optional): a TxDb object.

GTF_FILE (optional): GTF file which is used to built TXDB. If it is not specified, the function tries to extract from TXDB.

EXPR (optional): a matrix which contains expression values. Column names should be sample id and row names should be gene ids. Note gene ids in the expression matrix should be same type as genes in TxDb.

CHROMOSOME: a vector of chromosome names.

GENOME: abbreviation of GENOME.

GENOMIC_FEATURE_LIST: a list of genomic features as GRanges objects. There must be a element named 'cgi'.

MARKS (optional): a vector of ChIP-Seq markers.

methylation_hooks() must be defined.

chipseq_hooks() is optional unless you want to do integrative analysis.

CGI_SHORE_EXTEND: extension of cgi, by default it is 2kb both upstream and downstream.

register_global_var registers optional global variables.

Value

No value is returned.

Author(s)

Zuguang Gu <[e-mail]>

See Also

epik

Examples

# There is no example
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.