load_config: Load and validate configuration file
In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data
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
Examples
1
2
# There is no example
NULL
eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.
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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
Examples
1 2 | # There is no example
NULL
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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