chipseq-h3k4me3: ChIP-seq, H3K4me3 dataset results

In stephaniehicks/benchmarkfdrData2019: Data and Benchmarking Results from Korthauer and Kimes et al. (2019)

ChIP-seq, H3K4me3 dataset results

Description

Results for case study on differential peak calling in human H3K4me3 ChIP-seq data from ENCODE described in Korthauer and Kimes et al. (2019). Analyses were performed using either DESeq2 applied to predefined regions or with the csaw package.

Arguments

metadata

logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE)

Details

Results for this case study include:

• h3k4me3-promoters-benchmark: using predefined regions with mean coverage as covariate.

• h3k4me3-csaw-benchmark: using csaw with region width as covariate.

• h3k4me3-csaw-uninf-benchmark: using csaw with uninformative covariate.

• h3k4me3-csaw-cov-benchmark: using csaw with mean coverage as covariate.

See Also

chipseq-cbp

Examples

`h3k4me3-promoters-benchmark`(metadata = TRUE)

## Not run: 
`h3k4me3-promoters-benchmark`()
`h3k4me3-csaw-benchmark`()
`h3k4me3-csaw-uninf-benchmark`()
`h3k4me3-csaw-cov-benchmark`()

## End(Not run)

stephaniehicks/benchmarkfdrData2019 documentation built on April 13, 2025, 9:02 p.m.