Update README.md

README.md

@@ -35,27 +35,6 @@ Note that this strategy is currently only available for `hg19`, `hg38`, `mm9` an
 ### Introduction of CALDER analysis for other genomes
 
 Although CALDER was mainly tested on human and mouse dataset, it can be applied to dataset from other genomes. One additional information is required in such case: a `feature_track` 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.
-<br>
-<br>
-`feature_track` should be a data.frame or data.table of 4 columns (chr, start, end, score), and can be generated directly from conventional format such as bed or wig, see the following example:
-
-```
-library(rtracklayer)
-feature_track  = import('ENCFF934YOE.bigWig') ## from ENCODE https://www.encodeproject.org/files/ENCFF934YOE/@@download/ENCFF934YOE.bigWig
-feature_track = data.table::as.data.table(feature_track)[, c(1:3, 6)]
-```
-	> feature_track
-	chr	start	end	score
-	chr1	534179	534353	2.80512
-	chr1	534354	572399	0
-	chr1	572400	572574	2.80512
-	chr1	572575	628400	0
-	...	...	...	...
-	chrY	59031457	59032403	0
-	chrY	59032404	59032413	0.92023
-	chrY	59032414	59032415	0.96625
-	chrY	59032416	59032456	0.92023
-	chrY	59032457	59032578	0.78875
 
 # Installation
 
@@ -99,6 +78,7 @@ remotes::install_github("CSOgroup/CALDER")
 
 # Usage
 
+
 The input data of CALDER is a three-column text file storing the contact table of a full chromosome (zipped format is acceptable, as long as it can be read by `data.table::fread`). Each row represents a contact record `pos_x, pos_y, contact_value`, which is the same format as that generated by the `dump` command of juicer (https://github.com/aidenlab/juicer/wiki/Data-Extraction):	
 
 	16050000	16050000	10106.306
@@ -114,6 +94,26 @@ The input data of CALDER is a three-column text file storing the contact table o
 
 A demo dataset is included in the repository `CALDER/inst/extdata/mat_chr22_10kb_ob.txt.gz` and can be accessed by `system.file("extdata", "mat_chr22_10kb_ob.txt.gz", package='CALDER')` once CALDER is installed. This data contains contact values of GM12878 on chr22 binned at 10kb (Rao et al. 2014) 
 
+`feature_track` should be a data.frame or data.table of 4 columns (chr, start, end, score), and can be generated directly from conventional format such as bed or wig, see the following example:
+
+```
+library(rtracklayer)
+feature_track  = import('ENCFF934YOE.bigWig') ## from ENCODE https://www.encodeproject.org/files/ENCFF934YOE/@@download/ENCFF934YOE.bigWig
+feature_track = data.table::as.data.table(feature_track)[, c(1:3, 6)]
+```
+	> feature_track
+	chr	start	end	score
+	chr1	534179	534353	2.80512
+	chr1	534354	572399	0
+	chr1	572400	572574	2.80512
+	chr1	572575	628400	0
+	...	...	...	...
+	chrY	59031457	59032403	0
+	chrY	59032404	59032413	0.92023
+	chrY	59032414	59032415	0.96625
+	chrY	59032416	59032456	0.92023
+	chrY	59032457	59032578	0.78875
+
 CALDER contains three modules: (1) compute chromatin domains; (2) derive their hierarchical organization and obtain sub-compartments; (3) compute nested sub-domains within each compartment domain.
 
 ### Example one: use contact matrix file in dump format as input