6. Obtain various types of 1D metrics for the same sample

6.1 Calculation

# dense matrix
h1d multitypes IS,CI,DI \
	./test_data/GSE104334_Ctrl.chr21.matrix.gz \
	50000 chr21 -p 300000,300000,1000000 \
	--datatype matrix -o multi_types_metric
	
# .hic input
h1d multitypes IS,CI,DI \
	./test_data/GSE104334_Ctrl.hic  \
	50000 chr21 -p 300000,300000,1000000 \
	--datatype rawhic -o multi_types_metric --gt ./test_data/hg19_genome_table.txt 

# .cool input
h1d multitypes IS,CI,DI \
	./test_data/GSE104334_Ctrl.50000.cool  \
	50000 chr21 -p 300000,300000,1000000 \
	--datatype cool -o multi_types_metric --gt ./test_data/hg19_genome_table.txt

This will output a csv file multi_types_metric.csv like：

chr start end InsulationScore ContrastIndex DirectionalityIndex
... ... ... ... ... ...
chr21 23900000 23950000 0.652077 0.667196 -3.776812
chr21 23950000 24000000 0.636362 0.678699 -3.448456
... ... ... ... ... ...

6.2 Parameters

$ h1d multitypes
usage: h1d multitypes [-h] -p PARAMETER [-c CONTROLMATRIX]
                      [-o OUTNAME] [--datatype DATATYPE] [--gt GT]
                      [-d] [-s START] [-e END]
                      typelist data resolution chromosome

  • Required parameters:

    • typelist the list of types separated by comma.

      • When calculating one-sample metrics, it should be subset of [IS,CI,DI,SS,DLR,PC1,IES,IAS,IF].

      • When calculating two-sample metrics, it should be subset of [ISC,CIC,SSC,deltaDLR,CD,IESC,IASC,IFC,DRF]

    • data, Path of matrix file or raw .hic file

    • resolution, resolution (50000, i.e.) of given contact matrix, or choosed resolution for .hic file

    • chromosome, selected chromosome to be analyzed.

    • -p, list of parameters (comma-separated). Please refer to one-sample or two-sample metrics.

  • Optional parameters:

    • -o, output name, default: multitypes_metrics

    • -c, contact matrix or .hic file of control sample, which is required when calculating two-sample metrics.

    • --datatype, type of input data: “matrix” (default) or “rawhic”.

    • --gt, genome table file when using raw .hic data.

6.3 Visuliazation

-d, decide whether to plot.

-s, start site for plot.

-e, end site for plot.

  • Visulize one-sample metrics (output will be all_onesample.csv and all_onesample.pdf)

h1d multitypes IS,CI,DI,SS,DLR,PC1,IAS,IES,IF \
	./test_data/GSE104334_Ctrl.hic 50000 chr21 \
	-p 300000,300000,1000000,300000,3000000,./test_data/hg19_geneDensity50000.txt,300000,300000,0.05 
	--datatype rawhic --gt ./test_data/hg19_genome_table.txt 
	-o all_onesample -d -s 24500000 -e 34500000
RTDimport

  • Visulize two-sample metrics: (output will be all_twosample.csv and all_twosample.pdf)

h1d multitypes ISC,CIC,SSC,deltaDLR,CD,IASC,IESC,IFC,DRF \
	./test_data/GSE104334_Rad21KD.hic 50000 chr21 \
	-c ./test_data/GSE104334_Ctrl.hic \
	-p 300000,300000,300000,3000000,pearson,300000,300000,0.05,200000-5000000 \ 
	--datatype rawhic --gt ./test_data/hg19_genome_table.txt \
	-o all_twosample -d -s 24500000 -e 34500000
RTDimport