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FitHiChIP loop calls from human brain tissue

Source: R/get_CORCES2020_hichip_fithichip_loop_calls.R
get_CORCES2020_hichip_fithichip_loop_calls.Rd

FitHiChIP loop calls that overlap SNPs derived from analysis of H3K27ac HiChIP data. Each row represents an individual peak identified from the feature binarization analysis (see methods).

Usage

get_CORCES2020_hichip_fithichip_loop_calls()

Source

doi:10.1038/s41588-020-00721-x

Details

Data originally from Corces et al. (bioRxiv) (doi:10.1038/s41588-020-00721-x ), as of May 2020. Specifically: STable10_Coacessibility_Peak_loop_connection, HiChIP FitHiChIP Loop Calls sheet.

Column dictionary

hg38_Chromosome_Anchor1

The hg38 chromosome of the first loop Anchor.

hg38_Start_Anchor1

The hg38 start position of the first loop Anchor.

hg38_Stop_Anchor1

The hg38 stop position of the first loop Anchor.

Width_Anchor1

The width of the first loop Anchor.

hg38_Chromosome_Anchor2

The hg38 chromosome of the second loop Anchor.

hg38_Start_Anchor2

The hg38 start position of the second loop Anchor.

hg38_Stop_Anchor2

The hg38 stop position of the second loop Anchor.

Width_Anchor2

The width of the second loop Anchor.

Score

The -log10(q-value) of the loop call from FitHiChIP.

Anchor1_hasSNP

A boolean variable determining whether the first anchor overlaps a SNP from our AD/PD GWAS analyses.

Anchor2_hasSNP

A boolean variable determining whether the second anchor overlaps a SNP from our AD/PD GWAS analyses.

See also

Other CORCES2020: CORCES2020_get_ATAC_peak_overlap(), CORCES2020_get_hichip_fithichip_overlap(), CORCES2020_prepare_bulkATAC_peak_overlap(), CORCES2020_prepare_scATAC_peak_overlap(), get_CORCES2020_bulkATACseq_peaks(), get_CORCES2020_cicero_coaccessibility(), get_CORCES2020_scATACseq_celltype_peaks(), get_CORCES2020_scATACseq_peaks()

Examples

if (FALSE) { # \dontrun{
dat <- readxl::read_excel(
    file.path(
        "~/Desktop/Fine_Mapping/echolocatoR/annotations",
        "Coceres_2020/STable10_Coacessibility_Peak_loop_connection.xlsx"
    ),
    skip = 19, sheet = 1
)
CORCES2020_hichip_fithichip_loop_calls <- data.table::data.table(dat)

#### piggyback ####
tmp <- file.path(tempdir(), "CORCES2020_hichip_fithichip_loop_calls.tsv.gz")
data.table::fwrite(CORCES2020_hichip_fithichip_loop_calls, tmp, sep = "\t")
piggyback::pb_upload(
    file = tmp,
    repo = "RajLabMSSM/echoannot"
)
} # }