gencode.v30.b37.gene_density.50kbp: Gene density
In haizi-zh/hictools: Home-made handy tools for Hi-C
gencode.v30.b37.gene_density.50kbp R Documentation
Gene density
Description
Gene density data from gencode.v30.b37.gene_density. For a given interval,
indicate the number of genes overlapping with that interval.
Usage
gencode.v30.b37.gene_density.50kbp
gencode.v30.b37.gene_density.100kbp
gencode.v30.b37.gene_density.250kbp
gencode.v30.b37.gene_density.500kbp
gencode.v30.b37.gene_density.1000kbp
gencode.v30.b37.gene_density.250kbp
Format
An object of class GRanges of length 62072.
An object of class GRanges of length 31061.
An object of class GRanges of length 12459.
An object of class GRanges of length 6267.
An object of class GRanges of length 3173.
An object of class GRanges of length 12459.
Details
The dataset comes with various interval widths: 50 kbp, 100 kbp, 250 kbp, 500
kbp, 1000 kbp and 2500 kbp.
To prepare the dataset:
bedtools makewindows -g human_g1k_v37.chrom.sizes -w 500000 |
bedtools map -b gencode.v30.b37.gene_density.bedgraph -a - -c 4 -o count
Examples
data(gencode.v30.b37.gene_density.50kbp)
haizi-zh/hictools documentation built on June 29, 2022, 4:32 a.m.
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| gencode.v30.b37.gene_density.50kbp | R Documentation |
Gene density
Description
Gene density data from gencode.v30.b37.gene_density. For a given interval,
indicate the number of genes overlapping with that interval.
Usage
gencode.v30.b37.gene_density.50kbp gencode.v30.b37.gene_density.100kbp gencode.v30.b37.gene_density.250kbp gencode.v30.b37.gene_density.500kbp gencode.v30.b37.gene_density.1000kbp gencode.v30.b37.gene_density.250kbp
Format
An object of class GRanges of length 62072.
An object of class GRanges of length 31061.
An object of class GRanges of length 12459.
An object of class GRanges of length 6267.
An object of class GRanges of length 3173.
An object of class GRanges of length 12459.
Details
The dataset comes with various interval widths: 50 kbp, 100 kbp, 250 kbp, 500 kbp, 1000 kbp and 2500 kbp.
To prepare the dataset:
bedtools makewindows -g human_g1k_v37.chrom.sizes -w 500000 |
bedtools map -b gencode.v30.b37.gene_density.bedgraph -a - -c 4 -o count
Examples
data(gencode.v30.b37.gene_density.50kbp)
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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