|
|
@@ -34,7 +34,7 @@ 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. An example of `feature_track` is given in the **Usage** section
|
|
|
+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. An example of `feature_track` is given in the **Usage** section.
|
|
|
|
|
|
# Installation
|
|
|
|
|
|
@@ -79,7 +79,7 @@ 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):
|
|
|
+CALDER works on contact matrices in a three-column `dump` format of juicer (https://github.com/aidenlab/juicer/wiki/Data-Extraction):
|
|
|
|
|
|
16050000 16050000 10106.306
|
|
|
16050000 16060000 2259.247
|
|
|
@@ -92,8 +92,6 @@ The input data of CALDER is a three-column text file storing the contact table o
|
|
|
16070000 16080000 1996.749
|
|
|
...
|
|
|
|
|
|
-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:
|
|
|
|
|
|
```
|
Yuanlong LIU