finalRegions: Align peaks to form common regions then filter regions for...
In jnkoberstein/DEScan: Differential Enrichment Scan
Description
Usage
Arguments
Value
Description
Align peaks to form common regions then filter regions for presence in multiple replicates
Usage
1
2
finalRegions(peak_path, zthresh = 30, min_carriers = 2, chromosome = 1:19,
savefile = FALSE, keep_files = TRUE)
Arguments
peak_path
Path to peak files.
zthresh
Integer indicating minimum z-score considered significant
min_carriers
Integer indiciating the minimum number of replicates a region must be present in to be retained for testing
chromosome
Integer indicating which chromsomes to align. Defaults to all chromosomes.
savefile
Character indicating whether to save region files in the "bed" or "RData" format.
keep_files
Logical indicating whether to erase chromosome files after concatenating into a genome wide file.
Value
Matrix containing the regions as rows with columns for genomic coordinates, z-score and number of carriers.
jnkoberstein/DEScan documentation built on May 29, 2019, 11:39 a.m.
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Description Usage Arguments Value
Description
Align peaks to form common regions then filter regions for presence in multiple replicates
Usage
1 2 | finalRegions(peak_path, zthresh = 30, min_carriers = 2, chromosome = 1:19,
savefile = FALSE, keep_files = TRUE)
|
Arguments
peak_path |
Path to peak files. |
zthresh |
Integer indicating minimum z-score considered significant |
min_carriers |
Integer indiciating the minimum number of replicates a region must be present in to be retained for testing |
chromosome |
Integer indicating which chromsomes to align. Defaults to all chromosomes. |
savefile |
Character indicating whether to save region files in the "bed" or "RData" format. |
keep_files |
Logical indicating whether to erase chromosome files after concatenating into a genome wide file. |
Value
Matrix containing the regions as rows with columns for genomic coordinates, z-score and number of carriers.
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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