<xarray.Dataset> Size: 1GB
Dimensions: (configuration: 2, locus: 55220,
context: 96, component: 18,
shap_features: 19, shap_component: 18,
shap_locus: 2000, genome_state: 5,
feature: 19, sample: 736,
mesoscale_state: 9)
Coordinates:
* configuration (configuration) <U12 96B 'C/T-centered' '...
* locus (locus) int64 442kB 2 3 4 ... 65746 65747
* context (context) <U7 3kB 'A[C>A]A' ... 'T[T>C]T'
* component (component) <U3 216B 'M0' 'M1' ... 'M17'
* shap_features (shap_features) <U15 1kB 'ATACAccessible'...
* shap_component (shap_component) <U3 216B 'M0' ... 'M17'
* shap_locus (shap_locus) int64 16kB 24008 ... 22805
* genome_state (genome_state) <U30 600B 'Baseline' ... '...
* feature (feature) <U15 1kB 'ATACAccessible' ... '...
* sample (sample) <U19 56kB 'BR001.purple' ... 'TC...
Dimensions without coordinates: mesoscale_state
Data variables: (12/48)
Spectra/interactions (component, genome_state, context) float64 69kB ...
Spectra/shared_effects (component, genome_state) float64 720B 0....
Spectra/spectra (component, context, genome_state) float64 69kB ...
Regions/chrom (locus) <U4 884kB 'chr1' 'chr1' ... 'chr1'
Regions/start (locus) int64 442kB 819220 ... 248905601
Regions/end (locus) int64 442kB 820420 ... 248906235
... ...
State/mesoscale_idx (configuration, locus) int64 884kB 4 4 ... 4
State/log_context_distribution (component, context, mesoscale_state) float64 124kB ...
State/locus_features (locus, feature) float32 4MB 0.0 ... -0.1123
State/log_locus_distribution (component, locus) float64 8MB -0.6555 .....
ploidy (sample, locus) float32 0B <COO: nnz=0, fill_value=0.0>
X (sample, configuration, context, locus) float32 329MB <GCXS: nnz=329103, fill_value=0.0>
Attributes:
name: breast
dtype: sbs
genome_file: /n/data1/hms/dbmi/park/ctDNA_loci_project/locusregressio...
fasta_file: /n/data1/hms/dbmi/park/SOFTWARE/REFERENCE/hg38/cgap_matc...
blacklist_file: /n/data1/hms/dbmi/park/ctDNA_loci_project/locusregressio...
region_size: 10000
filename: retry2.nc
regions_file: ENFORM-Breast.nc.regions.bed| Format | gcxs |
|---|---|
| Data Type | float32 |
| Shape | (736, 2, 96, 55220) |
| nnz | 329103 |
| Density | 4.2175126691849206e-05 |
| Read-only | True |
| Size | 313.8M |
| Storage ratio | 0.01 |
| Compressed Axes | (0, 3) |
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[1.07627024e+00, 1.03581488e+00, 6.96110046e-01, 1.08464217e+00,
9.93231202e-01]],
[[1.16187166e+03, 1.40081319e+03, 9.97768810e+02, 1.16147823e+03,
1.29711305e+03],
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1.26219207e+02],
[4.43026885e+02, 4.50388211e+02, 3.82734162e+02, 4.42224897e+02,
4.95090831e+02],
...
[1.28919656e+00, 1.24454669e+00, 1.16317682e+00, 1.30077191e+00,
1.23202290e+00],
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8.66792636e+00],
[1.53090515e+00, 1.45388226e+00, 1.32933173e+00, 1.56705692e+00,
1.43355963e+00]],
[[1.93122719e+01, 1.89684112e+01, 1.70069389e+01, 2.16588199e+01,
1.98460245e+01],
[1.64461033e+01, 1.57246940e+01, 1.45577176e+01, 1.84358827e+01,
1.70138520e+01],
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1.75399219e+01],
...,
[1.47732826e+01, 1.42208827e+01, 1.30842463e+01, 1.65103017e+01,
1.52125593e+01],
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1.00295084e+01],
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1.11542159],
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1.13399989],
...,
[0.99581784, 0.80668588, 1.04100159, ..., 1.10980655, 1.04172925,
1.04570226],
[1.08037849, 0.8791703 , 1.18917993, ..., 1.00574662, 0.9642266 ,
1.11717325],
[1.06058621, 0.99303629, 0.80344021, ..., 0.94449919, 1.02351127,
0.84283685]])array([[4, 4, 4, ..., 4, 4, 4],
[4, 4, 4, ..., 4, 4, 4]])array([[[ 4.5962665 , 4.58637469, 4.51401636, ..., 4.07966074,
4.06976892, 3.99741059],
[ 2.19988997, 2.18907366, 2.11326877, ..., 1.81541568,
1.80459938, 1.72879449],
[ 5.22554881, 4.87865324, 4.76195561, ..., 4.76223853,
4.41534296, 4.29864534],
...,
[ 2.4939582 , 2.48314263, 2.40733781, ..., 2.1094841 ,
2.09866853, 2.02286371],
[ 2.50509506, 2.49427858, 2.41847369, ..., 2.12094571,
2.11012923, 2.03432434],
[ 3.70010277, 3.69235421, 3.61206082, ..., 3.3026668 ,
3.29491825, 3.21462485]],
[[11.5536536 , 11.55399227, 11.66410113, ..., 11.214367 ,
11.21470567, 11.32481453],
[ 9.03660751, 9.0439483 , 9.16672694, ..., 8.86861428,
8.87595508, 8.99873372],
[10.41748209, 10.41929398, 10.53040476, ..., 10.25471284,
10.25652473, 10.36763551],
...
[ 3.88487579, 3.87593712, 3.83057538, ..., 3.81725933,
3.80832066, 3.76295892],
[ 5.84955455, 5.84075493, 5.71967523, ..., 5.77309449,
5.76429488, 5.64321518],
[ 4.05474328, 4.03140316, 3.9657046 , ..., 3.96518224,
3.94184212, 3.87614356]],
[[ 7.36663111, 7.2519591 , 7.27922207, ..., 7.25747752,
7.14280551, 7.17006847],
[ 7.17862676, 7.06441642, 7.09835569, ..., 7.10151569,
6.98730534, 7.02124461],
[ 7.2542067 , 7.13393939, 7.13599822, ..., 7.17141878,
7.05115148, 7.0532103 ],
...,
[ 6.42304148, 6.31187726, 6.3411783 , ..., 6.33973892,
6.2285747 , 6.25787574],
[ 6.00265348, 5.89265615, 5.92458471, ..., 5.91771199,
5.80771466, 5.83964322],
[ 5.65154045, 5.54143411, 5.5725092 , ..., 5.56660132,
5.45649497, 5.48757006]]])array([[ 0. , 0.14334883, nan, ..., 0.37237236,
nan, 0.12899952],
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[ 0. , 0.28321943, nan, ..., 0.37237236,
1.3256534 , 0.12899952],
...,
[ 0. , -0.49613106, nan, ..., 0.6231408 ,
0.7472138 , 0.12271691],
[ 0. , -0.61278236, nan, ..., 0.6261261 ,
0.83775455, -0.11229002],
[ 0. , 3.2285004 , nan, ..., 0.6261261 ,
0.83775455, -0.11229002]], dtype=float32)array([[-0.65554925, -0.2438925 , -0.37652196, ..., 0.37380053,
-0.22485962, -1.59230489],
[-0.1627731 , -0.15052637, -0.1111911 , ..., 0.24952612,
-0.05667807, -0.40514609],
[ 0.01972296, 0.04950112, 0.06736122, ..., -0.04436633,
-0.00244809, 0.48643181],
...,
[-0.49480668, -0.46365254, -0.37882031, ..., 0.93277457,
0.32210232, -1.15851299],
[-0.6184988 , -0.77143883, -0.78516632, ..., 0.34161587,
-0.52125367, -1.08819858],
[-0.48760334, -0.66247436, -0.43428223, ..., -0.59671871,
-0.64300528, 0.21515802]])array(['C/T-centered', 'A/G-centered'], dtype='<U12')
array([ 2, 3, 4, ..., 65745, 65746, 65747])
array(['A[C>A]A', 'A[C>G]A', 'A[C>T]A', 'A[C>A]C', 'A[C>G]C', 'A[C>T]C',
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'C[C>A]A', 'C[C>G]A', 'C[C>T]A', 'C[C>A]C', 'C[C>G]C', 'C[C>T]C',
'C[C>A]G', 'C[C>G]G', 'C[C>T]G', 'C[C>A]T', 'C[C>G]T', 'C[C>T]T',
'G[C>A]A', 'G[C>G]A', 'G[C>T]A', 'G[C>A]C', 'G[C>G]C', 'G[C>T]C',
'G[C>A]G', 'G[C>G]G', 'G[C>T]G', 'G[C>A]T', 'G[C>G]T', 'G[C>T]T',
'T[C>A]A', 'T[C>G]A', 'T[C>T]A', 'T[C>A]C', 'T[C>G]C', 'T[C>T]C',
'T[C>A]G', 'T[C>G]G', 'T[C>T]G', 'T[C>A]T', 'T[C>G]T', 'T[C>T]T',
'A[T>A]A', 'A[T>G]A', 'A[T>C]A', 'A[T>A]C', 'A[T>G]C', 'A[T>C]C',
'A[T>A]G', 'A[T>G]G', 'A[T>C]G', 'A[T>A]T', 'A[T>G]T', 'A[T>C]T',
'C[T>A]A', 'C[T>G]A', 'C[T>C]A', 'C[T>A]C', 'C[T>G]C', 'C[T>C]C',
'C[T>A]G', 'C[T>G]G', 'C[T>C]G', 'C[T>A]T', 'C[T>G]T', 'C[T>C]T',
'G[T>A]A', 'G[T>G]A', 'G[T>C]A', 'G[T>A]C', 'G[T>G]C', 'G[T>C]C',
'G[T>A]G', 'G[T>G]G', 'G[T>C]G', 'G[T>A]T', 'G[T>G]T', 'G[T>C]T',
'T[T>A]A', 'T[T>G]A', 'T[T>C]A', 'T[T>A]C', 'T[T>G]C', 'T[T>C]C',
'T[T>A]G', 'T[T>G]G', 'T[T>C]G', 'T[T>A]T', 'T[T>G]T', 'T[T>C]T'],
dtype='<U7')array(['M0', 'M1', 'M2', 'M3', 'M4', 'M5', 'M6', 'M7', 'M8', 'M9', 'M10',
'M11', 'M12', 'M13', 'M14', 'M15', 'M16', 'M17'], dtype='<U3')array(['ATACAccessible', 'DNase', 'GeneExpression', 'H3K27ac', 'H3K27me3',
'H3K36me3', 'H3K4me1', 'H3K4me3', 'H3K9me3', 'POLR2A', 'GenePosition',
'RepliseqG1b', 'RepliseqG2', 'RepliseqS1', 'RepliseqS2', 'RepliseqS3',
'RepliseqS4', 'HICEigenvector', 'NucleotideRatio'], dtype='<U15')array(['M0', 'M1', 'M2', 'M3', 'M4', 'M5', 'M6', 'M7', 'M8', 'M9', 'M10',
'M11', 'M12', 'M13', 'M14', 'M15', 'M16', 'M17'], dtype='<U3')array([24008, 11878, 29922, ..., 1591, 51624, 22805])
array(['Baseline', 'GeneStrand:A/G-centered', 'GeneStrand:C/T-centered',
'ReplicationStrand:A/G-centered', 'ReplicationStrand:C/T-centered'],
dtype='<U30')array(['ATACAccessible', 'DNase', 'GeneExpression', 'H3K27ac', 'H3K27me3',
'H3K36me3', 'H3K4me1', 'H3K4me3', 'H3K9me3', 'POLR2A', 'GenePosition',
'RepliseqG1b', 'RepliseqG2', 'RepliseqS1', 'RepliseqS2', 'RepliseqS3',
'RepliseqS4', 'HICEigenvector', 'NucleotideRatio'], dtype='<U15')array(['BR001.purple', 'BR002.purple', 'BR003.purple', ...,
'TCGA-GI-A2C9.purple', 'TCGA-GM-A2DF.purple', 'TCGA-GM-A3XL.purple'],
dtype='<U19')PandasIndex(Index(['C/T-centered', 'A/G-centered'], dtype='object', name='configuration'))
PandasIndex(Index([ 2, 3, 4, 5, 6, 7, 8, 9, 12, 13,
...
65737, 65738, 65739, 65740, 65741, 65743, 65744, 65745, 65746, 65747],
dtype='int64', name='locus', length=55220))PandasIndex(Index(['A[C>A]A', 'A[C>G]A', 'A[C>T]A', 'A[C>A]C', 'A[C>G]C', 'A[C>T]C',
'A[C>A]G', 'A[C>G]G', 'A[C>T]G', 'A[C>A]T', 'A[C>G]T', 'A[C>T]T',
'C[C>A]A', 'C[C>G]A', 'C[C>T]A', 'C[C>A]C', 'C[C>G]C', 'C[C>T]C',
'C[C>A]G', 'C[C>G]G', 'C[C>T]G', 'C[C>A]T', 'C[C>G]T', 'C[C>T]T',
'G[C>A]A', 'G[C>G]A', 'G[C>T]A', 'G[C>A]C', 'G[C>G]C', 'G[C>T]C',
'G[C>A]G', 'G[C>G]G', 'G[C>T]G', 'G[C>A]T', 'G[C>G]T', 'G[C>T]T',
'T[C>A]A', 'T[C>G]A', 'T[C>T]A', 'T[C>A]C', 'T[C>G]C', 'T[C>T]C',
'T[C>A]G', 'T[C>G]G', 'T[C>T]G', 'T[C>A]T', 'T[C>G]T', 'T[C>T]T',
'A[T>A]A', 'A[T>G]A', 'A[T>C]A', 'A[T>A]C', 'A[T>G]C', 'A[T>C]C',
'A[T>A]G', 'A[T>G]G', 'A[T>C]G', 'A[T>A]T', 'A[T>G]T', 'A[T>C]T',
'C[T>A]A', 'C[T>G]A', 'C[T>C]A', 'C[T>A]C', 'C[T>G]C', 'C[T>C]C',
'C[T>A]G', 'C[T>G]G', 'C[T>C]G', 'C[T>A]T', 'C[T>G]T', 'C[T>C]T',
'G[T>A]A', 'G[T>G]A', 'G[T>C]A', 'G[T>A]C', 'G[T>G]C', 'G[T>C]C',
'G[T>A]G', 'G[T>G]G', 'G[T>C]G', 'G[T>A]T', 'G[T>G]T', 'G[T>C]T',
'T[T>A]A', 'T[T>G]A', 'T[T>C]A', 'T[T>A]C', 'T[T>G]C', 'T[T>C]C',
'T[T>A]G', 'T[T>G]G', 'T[T>C]G', 'T[T>A]T', 'T[T>G]T', 'T[T>C]T'],
dtype='object', name='context'))PandasIndex(Index(['M0', 'M1', 'M2', 'M3', 'M4', 'M5', 'M6', 'M7', 'M8', 'M9', 'M10',
'M11', 'M12', 'M13', 'M14', 'M15', 'M16', 'M17'],
dtype='object', name='component'))PandasIndex(Index(['ATACAccessible', 'DNase', 'GeneExpression', 'H3K27ac', 'H3K27me3',
'H3K36me3', 'H3K4me1', 'H3K4me3', 'H3K9me3', 'POLR2A', 'GenePosition',
'RepliseqG1b', 'RepliseqG2', 'RepliseqS1', 'RepliseqS2', 'RepliseqS3',
'RepliseqS4', 'HICEigenvector', 'NucleotideRatio'],
dtype='object', name='shap_features'))PandasIndex(Index(['M0', 'M1', 'M2', 'M3', 'M4', 'M5', 'M6', 'M7', 'M8', 'M9', 'M10',
'M11', 'M12', 'M13', 'M14', 'M15', 'M16', 'M17'],
dtype='object', name='shap_component'))PandasIndex(Index([24008, 11878, 29922, 58006, 41679, 19770, 47306, 65302, 34171, 15806,
...
48720, 40978, 32794, 34818, 39979, 56282, 48461, 1591, 51624, 22805],
dtype='int64', name='shap_locus', length=2000))PandasIndex(Index(['Baseline', 'GeneStrand:A/G-centered', 'GeneStrand:C/T-centered',
'ReplicationStrand:A/G-centered', 'ReplicationStrand:C/T-centered'],
dtype='object', name='genome_state'))PandasIndex(Index(['ATACAccessible', 'DNase', 'GeneExpression', 'H3K27ac', 'H3K27me3',
'H3K36me3', 'H3K4me1', 'H3K4me3', 'H3K9me3', 'POLR2A', 'GenePosition',
'RepliseqG1b', 'RepliseqG2', 'RepliseqS1', 'RepliseqS2', 'RepliseqS3',
'RepliseqS4', 'HICEigenvector', 'NucleotideRatio'],
dtype='object', name='feature'))PandasIndex(Index(['BR001.purple', 'BR002.purple', 'BR003.purple', 'BR004.purple',
'BR005.purple', 'BR006.purple', 'BR007.purple', 'BR008.purple',
'BR009.purple', 'BR010.purple',
...
'TCGA-E2-A1LL.purple', 'TCGA-E9-A1NH.purple', 'TCGA-EW-A1P8.purple',
'TCGA-EW-A1PB.purple', 'TCGA-EW-A1PC.purple', 'TCGA-EW-A1PH.purple',
'TCGA-EW-A3U0.purple', 'TCGA-GI-A2C9.purple', 'TCGA-GM-A2DF.purple',
'TCGA-GM-A3XL.purple'],
dtype='object', name='sample', length=736))