API Parameters

randno
  • http://progenetix.org/api?db=arraymap&collection=samples&api_out=ideogram&icdm_m=814&randno=100
  • retrieves a randomised subset of size n from the samples matched through the other parameters
  • new (05/2016): if multiple ICD-O codes are included, the randomisation will try to balance for equal representation of the different ICDs
    • if randno=100 and 4 ICD's with each >25 samples, it will result in 25 samples from each (25+25+25+25)
    • if one or several ICDs have fewer samples than their fractional share, all will be used and then the remainder filled from the larger sample groups (e.g. 10+15+38+37)

  • These parameters can be set to "-1" to exclude them from plots. The following call will plot a histogram (the default api_out parameter) without any additional markup.
  • http://arraymap.org/api/?db=arraymap&icdm_m=85&icdt_m=c50&randno=1000&ylab=-1&fstripw=-1&chrowidth=-1&maxy=55&footer=-1

API options (list represents RegEx matches used to stratify the API output):

api_doctype [
  json,
  png,
  svg,
  tab]
api_out [
  $_,
  \w,
  ^(\,?html)$,
  ^fsegments$,
  ^matrix$,
  ^matrixplot,
  ^segments$,
  ^valuematrix$,
  _meta_,
  apihelp,
  cgrouplist,
  connections,
  count,
  datakeys,
  fmatrixplot,
  gene(:?sample)?stats,
  genesamplestats,
  genesurv,
  histo,
  icdmlist,
  icdtlist,
  ideogram,
  platformlist,
  pubmap,
  samplemap,
  samples,
  seerlist,
  segments,
  surv]
api_params [
  ]
api_scope [
  platforms?,
  pub(lication)?s]


Query keys:

cellline_m:
  multiple "OR"; start-anchored CELLLINEID matches
cgroup_m:
  multiple "OR"; partial clinical group name matches, e.g. "colo"
dx_m:
  multiple "OR"; partial text matches queried over the diagnosis text
geo_m:
  location search
icdm_m:
  multiple "OR"; start-anchored ICD-O 3 matches, e.g. "817"
icdt_m:
  multiple "OR"; start-anchored ICD locus code matches, e.g. "50" for breast
locus_m:
  multiple "OR"; genomic locus (+/- CNA type) to be matched; e.g. "2:15998134-16004579:1" for samples with a MYCN gain/amplification
ncit_m:
  multiple "OR"; start-anchored NCIt code matches, e.g. "C27911" for "Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma"
platform_m:
  multiple "OR"; start-anchored array platform ID matches, e.g. "GPL60"
pmid_m:
  multiple "OR"; start-anchored PMID matches
seer_m:
  multiple "OR"; partial SEER group name matches
ser_m:
  multiple "OR"; start-anchored series ID matches, e.g. "GSE325"
tags_m:
  multiple "OR"
text_m:
  multiple "OR"; partial text matches queried over various attributes
uid_m:
  multiple "OR"; start-anchored UID matches
Topic revision: r6 - 01 Jun 2016, MichaelBaudis
This site is powered by FoswikiCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Progenetixwiki? Send feedback