Comments (6)
例子:
#### Usage
>>> import xenaPython as Xena
#### Examples
##### 1: Query four samples and three identifers expression
import xenaPython as xena
hub = "https://toil.xenahubs.net"
dataset = "tcga_RSEM_gene_tpm"
samples = ["TCGA-02-0047-01","TCGA-02-0055-01","TCGA-02-2483-01","TCGA-02-2485-01"]
probes = ['ENSG00000282740.1', 'ENSG00000000005.5', 'ENSG00000000419.12']
[position, [ENSG00000282740_1, ENSG00000000005_5, ENSG00000000419_12]] = xena.dataset_probe_values(hub, dataset, samples, probes)
ENSG00000282740_1
##### 2: Query four samples and three genes expression, when the dataset you want to query has a identifier-to-gene mapping (i.e. xena probeMap)
hub = "https://toil.xenahubs.net"
dataset = "tcga_RSEM_gene_tpm"
samples = ["TCGA-02-0047-01","TCGA-02-0055-01","TCGA-02-2483-01","TCGA-02-2485-01"]
genes =["TP53", "RB1", "PIK3CA"]
xena.dataset_gene_probe_avg(hub, dataset, samples, genes)
##### 3: If the dataset does not have id-to-gene mapping, but the dataset used gene names as its identifier, you can query gene expression like example 1, example 2 will not work.
hub = "https://toil.xenahubs.net"
dataset = "tcga_RSEM_Hugo_norm_count"
samples = ["TCGA-02-0047-01","TCGA-02-0055-01","TCGA-02-2483-01","TCGA-02-2485-01"]
probes =["TP53", "RB1", "PIK3CA"]
[position, [TP53, RB1, PIK3CA]] = xena.dataset_probe_values (hub, dataset, samples, probes)
TP53
##### 4: Find out the samples in a dataset
hub = "https://tcga.xenahubs.net"
dataset = "TCGA.BLCA.sampleMap/HiSeqV2"
xena.dataset_samples (hub, dataset, 10)
xena.dataset_samples (hub, dataset, None)
##### 5: Find out the identifiers in a dataset
hub = "https://tcga.xenahubs.net"
dataset = "TCGA.BLCA.sampleMap/HiSeqV2"
xena.dataset_field (hub, dataset)
##### 6. Find out the number of idnetifiers in a dataset
hub = "https://tcga.xenahubs.net"
dataset = "TCGA.BLCA.sampleMap/HiSeqV2"
xena.dataset_field_n (hub, dataset)
##### 7. Find out hub id, dataset id
use xena browser datasets tool: https://xenabrowser.net/datapages/
from ucscxenatools.
XenaData
的数据列ProbeMap
可以用于判断数据集是否有probemap,从来区分是否可以使用gene symbol进行检索。
from ucscxenatools.
The use cases have been introduced at the API documentation
from ucscxenatools.
希望能留个邮箱地址或者微信,方便请教
from ucscxenatools.
@CSUXu 邮箱主页就有。不过建议以Github issue进行讨论,这样更有针对性,也可以帮助其他人。
from ucscxenatools.
这些函数都已经在 v1.2.2中实现了,因此关闭issue。
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Related Issues (20)
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