2. Calculate 1D metrics for one sample

2.1 Quick start

h1d one IS ./test_data/GSE104334_Ctrl.chr21.matrix.gz \
		50000 chr21 -o Control_IS_chr21

This command would generate a bedGraph file (Control_IS_chr21.bedGraph) for Insulation Score. An example file can be download fron here

...	...	...
chr21	24300000	24350000	0.59419
chr21	24350000	24400000	0.604341
...	...	...

2.2 Usage

The analysis of one-sample metrics cound be run by h1d one sub-command :

$ h1d one -h # type -h for help
usage: h1d one [-h] [-p PARAMETER] [-o OUTNAME] [-d] [-s START] [-e END]
               [--datatype DATATYPE] [--gt GT] [--prefix PREFIX]
               [--maxchr MAXCHR] [-n NPROCESSER] [-t TADFILE]
               type data resolution chromosome

1D metrics designed for one Hi-C sample.

positional arguments:
  type                  Type of 1D metrics,,should be one of
                        {IS,CI,DI,SS,DLR,PC1,IES,IAS,IF}.
  data                  Path of matrix or rawhic file.
  resolution            Resolution of input matrix.
  chromosome            Chromosome number.

optional arguments:
  -h, --help            show this help message and exit
  -p PARAMETER, --parameter PARAMETER
                        Parameter for indicated metrics.
  -o OUTNAME, --outname OUTNAME
                        output name (default: 'metrics').
  -d, --draw            Plot figure for candidate region.
  -s START, --start START
                        Start sites for plotting.
  -e END, --end END     End sites for plotting.
  --datatype DATATYPE   Type of input data: [matrix(default),rawhic,cool]
  --msi MSI             Method for significant interactions: [fithic2,hiccups]
  --gt GT               genome_table file.
  --prefix PREFIX       ${prefix}chr1.matrix.gz
  --maxchr MAXCHR       Maximum index of chromosome (human genome is 22,i.e.)
  -n NPROCESSER, --nProcesser NPROCESSER
                        Number of processors
  -t TADFILE, --TADfile TADFILE
                        Give a TAD file, instead of using building-in TAD
                        calling method

type : type of 1D metrics could be one of {IS,CI,DI,SS,DLR,PC1,IES,IAS,IF}:
- Directional Index (DI) (PMID: 22495300)
- Insulation Score (IS) (PMID: 26030525)
- Contrast Index (CI) (PMID: 24981874)
- TAD separation score (SS) (PMID: 26431028)
- Distal-to-Local Ratio (DLR) (PMID: 30146161)
- Compartment PC1 (PC1) (PMID: 19815776)
- IntraTADscore (IAS) (Original metric)
- InterTADscore (IES) (Original metric)
- Interaction Frequency (IF)(Original metric)
Details is shown in our paper: link in the future
-p, --parameter for each 1D metric is :

Type	Description	default value
DI	length of bins	1000000
IS	square size	300000
CI	length of bins	300000
SS	length of bins	300000
DLR	Local distance	3000000
PC1	Gene density file	None
IAS	Paramter for TAD calling	300000
IES	Paramter for TAD calling	300000
IF	FDR threshold	0.05

Note !! : The sign of PC1 value is arbitrary unless provide a geneDensity file.

-t TADFILE, specify a TAD file (.bed format) to replace the built-in TAD calling method.
--msi, specify the method to calculate significant interactions. ‘fithic2’ (default) or ‘hiccups’ is supported.

2.3 Calculate 1D metrics (one-sample)

Use contact matrix:

h1d one CI ./test_data/GSE104334_Ctrl.chr21.matrix.gz \
	50000 chr21 -p 300000 -o control_CI_chr21 --datatype matrix

Use raw .hic file:

h1d one CI ./test_data/GSE104334_Ctrl.hic \
	50000 chr21  -p 300000 -o control_CI_chr21 --datatype rawhic \
	--gt ./test_data/hg19_genome_table.txt	

Use raw .cool file

h1d one CI ./test_data/GSE104334_Ctrl.50000.cool \
	50000 chr21 -p 300000 -o control_CI_chr21 --datatype cool
	--gt ./test_data/hg19_genome_table.txt

Output will be control_CI_chr21.bedGraph as described before.

Calculation of IF only support rawhic datatype

Multiprocessing for all chromomes:

To deal with multiple chromosomes, you should first use dump function in h1d.

To run all chromosomes parallel, do:

h1d one IS ./test/Control/ 50000 all 
	--maxchr 22 --prefix observed.KR. -n 30 -o control

chromosome , set chromosome to “all” will compute metrics for all chromosomes.
data, if calculating for all chromosomes, the input file should be absolute folder of contact matrix.
-maxchr, Maximum index of chromosome (human genome is 22,i.e.). It will compute chromosome 1~maxchr plus chromosome X.

--prefix, the prefix of matrix file, please modify the name of zipped matrix to ${prefix}chr1.matrix.gz. If you used our dump function, the file should be:

├── observed.KR.chr1.matrix.gz
├── observed.KR.chr10.matrix.gz
├── observed.KR.chr11.matrix.gz
├── observed.KR.chr12.matrix.gz
├── observed.KR.chr13.matrix.gz
├── observed.KR.chr14.matrix.gz

so the prefix is observed.KR.

-n, Number of processors

Output would be control_IS_allchr.csv.

2.4 Visulize 1D metrics (one-sample)

Use contact matrix:

h1d one CI ./test_data/GSE104334_Ctrl.chr21.matrix.gz \
	50000 chr21 -p 300000 -o Control_CI_chr21 --datatype matrix \
  --draw -s 26000000 -e 33000000

Use raw hic:

h1d one CI ./test_data/GSE104334_Ctrl.hic \
	50000 chr21 -p 300000 -o Control_CI_chr21 --datatype rawhic \
	--gt ./test_data/hg19_genome_table.txt --draw -s 26000000 -e 33000000

Use cool file:

h1d one CI ./test_data/GSE104334_Ctrl.50000.cool \
	50000 chr21 -p 300000 -o Control_CI_chr21 --datatype cool \
	--gt ./test_data/hg19_genome_table.txt --draw -s 26000000 -e 33000000

The output will be control_CI_chr21.bedGraph and control_CI_chr21.pdf:

RTDimport