triform: Run Triform peak detection algorithm.

In triform: Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data

Description

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

Usage

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:

• COVER.PATH Path for coverage files (from preprocessing).

• OUTPUT.PATH Path for output file.

• TARGETS Filenames for TF experiments. (Named according to replicate, i.e. myTF_rep1.bed for replicate 1.

• CONTROLS Filnames for control experiments (Named according to replicate).

• MAX.P Minimum p-value, used to calculate min.z

• MIN.WIDTH Minimum peak width (min.n)

• MIN.QUANT Quantile of enrichment ratios, used to calculate min.er

• MIN.SHIFT Minimum inter-strand lag between peak coverage distributions.

• FLANK.DELTA Fixed spacing between central and flanking locations.

• CHRS A list of chromosomes to be processed.

Value

Output is saved to the outputpath.

Author(s)

Karl Kornacker <[e-mail]> and Tony Handstad <[e-mail]>

See Also

preprocess

Examples

## 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 April 28, 2020, 7 p.m.