triform: Run Triform peak detection algorithm.

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

View source: R/triform.R

Description

Runs Triform according to configuration file or given parameters.
Triform uses chromosome coverage files prepared by the preprocessing function.

Usage

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triform(configPath = "./config.yml", params=list())

Arguments

configPath

Path to a configuration file in YAML format, or NULL.

params

A list of parameters values (see details)

Details

If configPath is NULL, all the other arguments must be supplied in params.
Values in params will overwrite values as set in the configuration file. The following list explains the parameters for the triform algorithm:

Value

Output is saved to the outputpath.

Author(s)

Karl Kornacker <[email protected]> and Tony Handstad <[email protected]>

See Also

preprocess

Examples

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## Not run: 
# Run Triform with configuration file:
triform(configPath = "./config.yml")

# Run Triform with arguments instead of configuration file:
triform(configPath=NULL, params=list(COVER.PATH = "./chrcovers",
       OUTPUT.PATH = "./Triform_output.csv",
       CONTROLS = c("backgr_huds_Gm12878_rep1", "backgr_huds_Gm12878_rep2"),
       TARGETS = c("srf_huds_Gm12878_rep1", "srf_huds_Gm12878_rep2"),
       MAX.P = 0.1, MIN.WIDTH = 10, MIN.QUANT = 0.375, MIN.SHIFT = 10, 
       FLANK.DELTA = 150, CHRS = c("chrY")))

## End(Not run)

triform documentation built on Nov. 1, 2018, 2:25 a.m.