roadmap/docs/04.hilbert_curve_diff.md

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Visualize global difference by Hilbert curve

First we configure how to read data:

source("~/project/development/epik/roadmap/data_config.R")

gr_meth = hilbert_curve_methylation_difference(subgroup = SUBGROUP,
    comparison = c("group1", "group2"), type = c("global_mean", "subgroup_mean", "difference"))

gr_meth

## GRanges object with 2881044 ranges and 3 metadata columns:
##             seqnames               ranges strand | mean_group1 mean_group2
##                <Rle>            <IRanges>  <Rle> |   <numeric>   <numeric>
##         [1]     chr1         [   1, 1000]      * |         NaN         NaN
##         [2]     chr1         [1001, 2000]      * |         NaN         NaN
##         [3]     chr1         [2001, 3000]      * |         NaN         NaN
##         [4]     chr1         [3001, 4000]      * |         NaN         NaN
##         [5]     chr1         [4001, 5000]      * |         NaN         NaN
##         ...      ...                  ...    ... .         ...         ...
##   [2881040]    chr22 [51300001, 51301000]      * |         NaN         NaN
##   [2881041]    chr22 [51301001, 51302000]      * |         NaN         NaN
##   [2881042]    chr22 [51302001, 51303000]      * |         NaN         NaN
##   [2881043]    chr22 [51303001, 51304000]      * |         NaN         NaN
##   [2881044]    chr22 [51304001, 51304566]      * |         NaN         NaN
##                  mean
##             <numeric>
##         [1]       NaN
##         [2]       NaN
##         [3]       NaN
##         [4]       NaN
##         [5]       NaN
##         ...       ...
##   [2881040]       NaN
##   [2881041]       NaN
##   [2881042]       NaN
##   [2881043]       NaN
##   [2881044]       NaN
##   -------
##   seqinfo: 22 sequences from an unspecified genome; no seqlengths

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.