BioCyc 富集分析 — biocyc_enrichment • cailab.utils

使用 BioCyc 的 SmartTables 服务进行富集分析

Usage

biocyc_enrichment(
  session,
  method = c("GET", "PUT"),
  table_id = NULL,
  key = "enrich-genes-pwys",
  type = "enrichment",
  threshold = 0.1,
  statistic = "fisher-exact",
  correction = "none",
  class = "Genes",
  orgid = "ECOLI",
  values = c("trpA", "trpB")
)

Arguments

session: httr::handle对象，表示已建立的BioCyc会话
method: 字符串，指定使用的方法，可选 "GET" 或 "PUT"（默认为 "GET"）
table_id: 字符串，SmartTable 标识符（仅在 method="GET" 时使用）
key: 字符串，富集分析类型，可选值包括 "enrich-all-gen", "enrich-go-cc", "enrich-go-bp", "enrich-go-mf", "enrich-genes-regulators-indirect", "enrich-genes-regulators", "enrich-cpds-pwys", 或 "enrich-genes-pwys"
type: 字符串，分析类型，可选 "enrichment"、"depletion" 或 "enrichment-and-depletion"（默认为 "enrichment"）
threshold: 数值，P 值阈值，介于 0 和 1 之间（默认为 0.1）
statistic: 字符串，统计方法，可选 "fisher-exact"（默认）、"parent-child-union" 或 "parent-child-intersection"
correction: 字符串，多重检验校正方法，可选 "none"（默认）、"bonferroni"、"bh"（Benjamini-Hochberg）或 "by"（Benjamini-Yekutieli）
class: 字符串，数据类型，可选 "Genes" 或 "Compounds"（仅在 method="PUT" 且 format="tsv" 时使用）
orgid: 字符串，指定生物体的 BioCyc ID，例如 "ECOLI" 代表大肠杆菌
values: 字符向量，包含要分析的基因列表

Value

数据框，包含富集分析结果

Details

With the GET method, runs an enrichment analysis on the first column of an existing SmartTable. To upload a file of genes or compounds and run an enrichment analysis on it in one step, use the PUT method, and also supply the args needed for the st-create service.

Mode Arguments:

Both: key, type, threshold, statistic, correction
With GET: id
With PUT: orgid, class, values

Arguments:

key: one value from enrich-all-gen, enrich-go-cc, enrich-go-bp, enrich-go-mf, enrich-genes-regulators-indirect, enrich-genes-regulators, enrich-cpds-pwys, or enrich-genes-pwys (Both)
type: enrichment, depletion, or enrichment-and-depletion (Both)
threshold: a number between 0 and 1; only include results with P-value less than this number (default = 0.1) (Both)
statistic: fisher-exact (default), parent-child-union, or parent-child-intersection
correction: none (default), bonferroni, bh (Benjamini-Hochberg), or by (Benjamini-Yekutieli)
id: SmartTable ID (GET only)
class: Genes or Compounds (PUT only)
orgid: the identifier for the organism database (PUT only)
values: an array of strings, which will be coerced into objects for the SmartTable in a single column (PUT only)

Examples

if (FALSE) { # \dontrun{
# 使用 GET 方法
result_get = biocyc_enrichment(method = "GET", 
                 table_id = "your_table_id", 
                 key = "enrich-all-gen", 
                 organism_id = "ECOLI", 
                 session = session)
print(result_get)

# 使用 PUT 方法
gene_list = c("gene1", "gene2", "gene3")
result_put = biocyc_enrichment(method = "PUT", 
                               gene_list = gene_list, 
                               key = "enrich-genes-pwys", 
                               organism_id = "ECOLI", 
                               session = session, 
                               format = "tsv", 
                               class = "Genes")
print(result_put)
} # }