View source: R/ReturnPathwaysEnrich_InputAnalytes.R
runCombinedFisherTest | R Documentation |
Do fisher test for only one pathway from search result clicked on highchart
runCombinedFisherTest(
db = RaMP(),
analytes,
NameOrIds = "ids",
total_genes = 20000,
min_analyte = 2,
MCall = F,
alternative = "less",
min_path_size = 5,
max_path_size = 150,
includeRaMPids = FALSE,
background_type = "database",
background = "database",
pathway_definitions = "RaMP",
include_smpdb = FALSE
)
db |
a RaMP databse object |
analytes |
a vector of analytes (genes or metabolites) that need to be searched |
NameOrIds |
whether input is "names" or "ids" (default is "ids", must be the same for analytes and background) |
total_genes |
number of genes analyzed in the experiment (e.g. background) (default is 20000, with assumption that analyte_type is "genes") |
min_analyte |
if the number of analytes (gene or metabolite) in a pathway is < min_analyte, do not report |
MCall |
T/F if true, all pathways are used for multiple comparison corrections; if false, only pathways covering user analytes will be used (default is "F") |
alternative |
alternative hypothesis test passed on to fisher.test(). Options are two.sided, greater, or less (default is "less") |
min_path_size |
the minimum number of pathway members (genes and metabolites) to include the pathway in the output (default = 5) |
max_path_size |
the maximum number of pathway memnbers (genes and metaboltes) to include the pathway in the output (default = 150) |
includeRaMPids |
include internal RaMP identifiers (default is "FALSE") |
background_type |
type of background that is input by the user. Opions are "database" if user wants all analytes from the RaMP database to be used as background; "file", if user wnats to input a file path with a list of background analytes; "list", if user wants to input a vector of analyte IDs; "biospecimen", if user wants to specify a biospecimen type (e.g. blood, adipose tissue, etc.) and have those biospecimen-specific analytes used. For genes, only the "database" option is used. |
background |
background to be used for Fisher's tests. If parameter 'background_type="database"', this parameter is ignored (default="database"); if parameter 'background_type= "file"', then 'background' should be a file name (with directory); if 'background_type="list"', then 'background' should be a vector of RaMP IDs; if 'backgroud_type="biospecimen"' then users should specify one of the following: "Blood", "Adipose tissue", "Heart", "Urine", "Brain", "Liver", "Kidney", "Saliva", and "Feces" |
pathway_definitions |
If "RaMP" (default), use pathway definitions within RaMP-DB. Else, supply path to gmx file containing custom pathway definitions. GMX files are a tab-separated format that contain one analyte set per column, with the name of the set in the first row, and constituent analytes in subsequent rows. Please supply a .xls or .xlsx file. If supplying pathway definitions for genes and metabolites, ensure that metabolite definitions are on tab 1, and gene definitions are on tab2. |
include_smpdb |
Include pathways from smpdb/hmdb in analysis. Excluded by default since definitions are highly redundant |
a list containing two entries: [[1]] fishresults, a dataframe containing pathways with Fisher's p values (raw and with FDR and Holm adjustment), number of user analytes in pathway, total number of analytes in pathway, and pathway source ID/database. [[2]] analyte_type, a string specifying the type of analyte input into the function ("genes", "metabolites", or "both")
## Not run:
pkg.globals <- setConnectionToRaMP(
dbname = "ramp2", username = "root",
conpass = "", host = "localhost"
)
analyte.list <- c(
"chebi:15344", "chebi:10983", "chebi:15351",
"uniprot:Q86V21", "uniprot:Q02338", "uniprot:Q9BUT1"
)
fisher.results <- runCombinedFisherTest(analytes = analyte.list, NameOrIds = "ids")
## End(Not run)
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