load_config: Load and validate configuration file

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Load and validate configuration file

Usage

1
load_config(config_file, export_env = parent.frame(), validate = TRUE)

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_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 species.

OUTPUT_DIR: path of output directory. Several sub directories will be created.

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.

CR_CUTOFF: cutoff for correlation significance of cr.

Value

No value is returned.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

See Also

epic

Examples

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# There is no example
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eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.