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Update README.md

Yuanlong LIU 3 years ago
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2e1e85471f
1 changed files with 4 additions and 1 deletions
  1. 4 1
      README.md

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README.md

@@ -36,7 +36,10 @@ Note that this strategy is currently only available for `hg19`, `hg38`, `mm9` an
 
 
 Although CALDER was mainly tested on human and mouse dataset, it can be applied on dataset from other genomes. One additional information is required in such case: a `feature_track` that is presumably positively correlated with compartment score (thus higher values in A than in B compartment). This information will be used for correctly determing the `A/B` direction. Some suggested tracks are gene density, H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K36me3 (or negative transform of H3K9me3) signals. Note that this information will not alter the hierarchical compartment/TAD structure, and can come from any external study with matched genome.
 Although CALDER was mainly tested on human and mouse dataset, it can be applied on dataset from other genomes. One additional information is required in such case: a `feature_track` that is presumably positively correlated with compartment score (thus higher values in A than in B compartment). This information will be used for correctly determing the `A/B` direction. Some suggested tracks are gene density, H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K36me3 (or negative transform of H3K9me3) signals. Note that this information will not alter the hierarchical compartment/TAD structure, and can come from any external study with matched genome.
 
 
-rtracklayer
+
+	library(rtracklayer)
+    feature_track  = import('/mnt/etemp/Yuanlong/4.Tmp/ENCFF934YOE.bigWig')
+    feature_track = data.table::as.data.table(feature_track)[, c(1:3, 6)]
 
 
 	chr	start	end	score
 	chr	start	end	score
 	chr1	534179	534353	2.80512
 	chr1	534179	534353	2.80512