【r<-包】UCSCXenaTools：Xena的R AP
2019-03-30 本文已影响22人
王诗翔
很久没有更新简书了～最近除了课题分析，我把主要精力放在Xena API的实现上，现在终于算是成功了。
提供API有什么好处：你不再需要下载整个数据集了！你可以搜索你感兴趣基因的表达值以及其他Xena提供的各种信息。不过我实现和开放API函数的主要目的是为了方便和小伙伴一起开发XenaShiny应用，对于不懂编程的用户，那将是更友好的分析工具！
目前我开放了接近50个API函数，大多数是低级的，后续更新的一个任务就是根据频次需要构建一些高级的API函数。
| Original Name | Function Name | Level | Description |
|---|---|---|---|
| cohorts | cohorts | Higher | Return cohorts as character vector |
| datasets | datasets | Higher | Return datasets as character vector |
| hosts | hosts | Higher | Return hosts as character vector |
| samples | samples | Higher | Return samples according to “by” and “how” option |
| .cohort_datasets | .cohort_datasets | Lower | Return datasets of cohorts |
| .cohort_datasets_count | .cohort_datasets_count | Lower | Return dataset count of cohorts |
| .cohort_samples_all | .cohort_samples_all | Lower | Return samples shared by all cohort |
| .cohort_samples_any | .cohort_samples_any | Lower | Return samples present any cohort |
| .cohort_samples_each | .cohort_samples_each | Lower | Return samples present in each cohort |
| .dataset_samples_all | .dataset_samples_all | Lower | Return samples shared by all dataset |
| .dataset_samples_any | .dataset_samples_any | Lower | Return samples present in any cohort |
| .dataset_samples_each | .dataset_samples_each | Lower | Return samples present in each dataset |
| .host_cohorts | .host_cohorts | Lower | Return cohorts of hosts |
| all_datasets_n | .p_all_datasets_n | Lower | Count the number datasets with non-null cohort |
| all_field_metadata | .p_all_field_metadata | Lower | Metadata for all dataset fields (phenotypic datasets) |
| cohort_samples | .p_cohort_samples | Lower | All samples in cohort |
| cohort_summary | .p_cohort_summary | Lower | Count datasets per-cohort, excluding the given dataset types |
| dataset_fetch | .p_dataset_fetch | Lower | Probe values for give samples |
| dataset_field | .p_dataset_field | Lower | All field (probe) names in dataset |
| dataset_field_examples | .p_dataset_field_examples | Lower | Field names in dataset, up to |
| dataset_field_n | .p_dataset_field_n | Lower | Number of fields in dataset |
| dataset_gene_probe_avg | .p_dataset_gene_probe_avg | Lower | Probe average, per-gene, for given samples |
| dataset_gene_probes_values | .p_dataset_gene_probes_values | Lower | Probe values in gene, and probe genomic positions, for given samples |
| dataset_list | .p_dataset_list | Lower | Dataset metadata for datasets in the given cohorts |
| dataset_metadata | .p_dataset_metadata | Lower | Dataset metadata |
| dataset_probe_signature | .p_dataset_probe_signature | Lower | Computed probe signature for given samples and weight array |
| dataset_probe_values | .p_dataset_probe_values | Lower | Probe values for given samples, and probe genomic positions |
| dataset_samples | .p_dataset_samples | Lower | All samples in dataset (optional limit) |
| feature_list | .p_feature_list | Lower | Dataset field names and long titles (phenotypic datasets) |
| field_codes | .p_field_codes | Lower | Codes for categorical fields |
| field_metadata | .p_field_metadata | Lower | Metadata for given fields (phenotypic datasets) |
| gene_transcripts | .p_gene_transcripts | Lower | Gene transcripts |
| match_fields | .p_match_fields | Lower | Find fields matching names (must be lower-case) |
| probemap_list | .p_probemap_list | Lower | Find probemaps |
| ref_gene_exons | .p_ref_gene_exons | Lower | Gene model |
| ref_gene_position | .p_ref_gene_position | Lower | Gene position from gene model |
| ref_gene_range | .p_ref_gene_range | Lower | Gene models overlapping range |
| segment_data_examples | .p_segment_data_examples | Lower | Initial segmented data rows, with limit |
| segmented_data_range | .p_segmented_data_range | Lower | Segmented (copy number) data overlapping range |
| sparse_data | .p_sparse_data | Lower | Sparse (mutation) data rows for genes |
| sparse_data_examples | .p_sparse_data_examples | Lower | Initial sparse data rows, with limit |
| sparse_data_match_field | .p_sparse_data_match_field | Lower | Genes in sparse (mutation) dataset matching given names |
| sparse_data_match_field_slow | .p_sparse_data_match_field_slow | Lower | Genes in sparse (mutation) dataset matching given names, case-insensitive (names must be lower-case) |
| sparse_data_match_partial_field | .p_sparse_data_match_partial_field | Lower | Partial match genes in sparse (mutation) dataset |
| sparse_data_range | .p_sparse_data_range | Lower | Sparse (mutation) data rows overlapping the given range, for the given samples |
更详细的信息查看文档https://shixiangwang.github.io/UCSCXenaTools/articles/xena-apis.html关于API的文章。
