def filter_expr(meth, series_obj_id=None, filtering_method="anova",
num_genes=None, p_value="1.0"):
"""Filter expression table to differentially expressed genes
:param series_obj_id:Object id of the expression series data
:type series_obj_id:kbtypes.KBaseExpression.ExpressionSeries
:param filtering_method: Filtering method ('anova' for ANOVA or 'lor' for log-odd ratio)
:type filtering_method: kbtypes.Unicode
:param num_genes: Target number of genes (choose this or p-value below)
:type num_genes: kbtypes.Unicode
:param p_value: p-value cutoff (choose this or num_genes above)
:type p_value: kbtypes.Unicode
:return: Workspace id
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
meth.stages = 3
meth.advance("Initialize COEX service")
cc = CoExpression(URLS.coex, token=meth.token)
argsx = {"ws_id" : meth.workspace_id, "inobj_id" : series_obj_id, "outobj_id" : series_obj_id+".fltrd", "p_value" : "0.05", "method" : filtering_method, "num_genes" : num_genes}
meth.advance("submit job to select genes")
try:
jid = cc.filter_genes(argsx)
except Exception as err:
raise COEXException("submit job failed: {}".format(err))
if not jid:
raise COEXException(2, "submit job failed, no job id")
AweJob.URL = URLS.awe
AweJob(meth, started="Differential expression filter", running="Differential expression filter").run(jid[0])
return _workspace_output(series_obj_id+".fltrd")
def build_net_clust(meth,
series_obj_id=None,
net_method='simple',
clust_method='hclust',
cut_off=None,
num_module=None):
"""Construct co-expression network and a set of densely interconnected clusters in co-expression network based on
expression table object
:param series_obj_id: Object id of the expression Series data
:type series_obj_id: kbtypes.KBaseExpression.ExpressionSeries
:param net_method : Network construction algorithm ('simple' for Pearson correlation coefficient or 'WGCNA')
:type net_method: kbtypes.Unicode
:param clust_method : Clustering algorithm ('hclust' for hierachical clustering or 'WGNCA')
:type clust_method: kbtypes.Unicode
:param cut_off: Lower cutoff to keep edges
:type cut_off: kbtypes.Unicode
:param num_module: The number of cluster
:type num_module: kbtypes.Unicode
:return: Workspace id
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
meth.stages = 3
meth.advance("Initialize COEX service")
cc = CoExpression(URLS.coex, token=meth.token)
argsx = {
"ws_id": meth.workspace_id,
"inobj_id": series_obj_id,
"outobj_id": 'coex_by_' + series_obj_id,
"cut_off": cut_off,
"net_method": net_method,
"clust_method": clust_method,
"num_modules": num_module
}
meth.advance("submit job to construct network and clusters")
try:
jid = cc.const_coex_net_clust(argsx)
except Exception as err:
raise COEXException("submit job failed: {}".format(err))
if not jid:
raise COEXException(2, "submit job failed, no job id")
AweJob.URL = URLS.awe
AweJob(meth,
started="Construct coex network and clusters",
running="Construct coex network and clusters").run(jid[0])
return _workspace_output('coex_by_' + series_obj_id)
def filter_expr(meth,
series_obj_id=None,
filtering_method="anova",
num_genes=None,
p_value="1.0"):
"""Filter expression table to differentially expressed genes
:param series_obj_id:Object id of the expression series data
:type series_obj_id:kbtypes.KBaseExpression.ExpressionSeries
:param filtering_method: Filtering method ('anova' for ANOVA or 'lor' for log-odd ratio)
:type filtering_method: kbtypes.Unicode
:param num_genes: Target number of genes (choose this or p-value below)
:type num_genes: kbtypes.Unicode
:param p_value: p-value cutoff (choose this or num_genes above)
:type p_value: kbtypes.Unicode
:return: Workspace id
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
meth.stages = 3
meth.advance("Initialize COEX service")
cc = CoExpression(URLS.coex, token=meth.token)
argsx = {
"ws_id": meth.workspace_id,
"inobj_id": series_obj_id,
"outobj_id": series_obj_id + ".fltrd",
"p_value": "0.05",
"method": filtering_method,
"num_genes": num_genes
}
meth.advance("submit job to select genes")
try:
jid = cc.filter_genes(argsx)
except Exception as err:
raise COEXException("submit job failed: {}".format(err))
if not jid:
raise COEXException(2, "submit job failed, no job id")
AweJob.URL = URLS.awe
AweJob(meth,
started="Differential expression filter",
running="Differential expression filter").run(jid[0])
return _workspace_output(series_obj_id + ".fltrd")
def build_net_clust(meth, series_obj_id=None, net_method='simple', clust_method='hclust',
cut_off=None, num_module=None):
"""Construct co-expression network and a set of densely interconnected clusters in co-expression network based on
expression table object
:param series_obj_id: Object id of the expression Series data
:type series_obj_id: kbtypes.KBaseExpression.ExpressionSeries
:param net_method : Network construction algorithm ('simple' for Pearson correlation coefficient or 'WGCNA')
:type net_method: kbtypes.Unicode
:param clust_method : Clustering algorithm ('hclust' for hierachical clustering or 'WGNCA')
:type clust_method: kbtypes.Unicode
:param cut_off: Lower cutoff to keep edges
:type cut_off: kbtypes.Unicode
:param num_module: The number of cluster
:type num_module: kbtypes.Unicode
:return: Workspace id
:rtype: kbtypes.Unicode
:output_widget: ValueListWidget
"""
meth.stages = 3
meth.advance("Initialize COEX service")
cc = CoExpression(URLS.coex, token=meth.token)
argsx = {"ws_id" : meth.workspace_id, "inobj_id" : series_obj_id, "outobj_id" : 'coex_by_' +series_obj_id, "cut_off" : cut_off, "net_method" : net_method, "clust_method" : clust_method, "num_modules" : num_module}
meth.advance("submit job to construct network and clusters")
try:
jid = cc.const_coex_net_clust(argsx)
except Exception as err:
raise COEXException("submit job failed: {}".format(err))
if not jid:
raise COEXException(2, "submit job failed, no job id")
AweJob.URL = URLS.awe
AweJob(meth, started="Construct coex network and clusters", running="Construct coex network and clusters").run(jid[0])
return _workspace_output('coex_by_' +series_obj_id)