compose_description_v1.4.2 | R Documentation |
Compose BioCompute Object - Description Domain (v1.4.2)
compose_description_v1.4.2( keywords = NULL, xref = NULL, platform = list("Seven Bridges Platform"), pipeline_meta = NULL, pipeline_prerequisite = NULL, pipeline_input = NULL, pipeline_output = NULL ) compose_description( keywords = NULL, xref = NULL, platform = list("Seven Bridges Platform"), pipeline_meta = NULL, pipeline_prerequisite = NULL, pipeline_input = NULL, pipeline_output = NULL )
keywords |
Character vector. A list of keywords to aid in searchability and description of the experiment. |
xref |
Data frame. A list of the databases and/or ontology IDs that are cross-referenced in the BCO. |
platform |
Character string or list. Reference to a particular deployment of an existing platform where this BCO can be reproduced. |
pipeline_meta |
Data frame. Pipeline metadata.
Variables include |
pipeline_prerequisite |
Data frame. Packages or prerequisites
for running the tools used. Variables include |
pipeline_input |
Data frame. Input files for the tools.
Variables include |
pipeline_output |
Data frame. Output files for the tools.
Variables include |
A list of class bco.domain
keywords <- c("HCV1a", "Ledipasvir", "antiviral resistance", "SNP", "amino acid substitutions") xref <- data.frame( "namespace" = c("pubchem.compound", "pubmed", "so", "taxonomy"), "name" = c("PubChem-compound", "PubMed", "Sequence Ontology", "Taxonomy"), "ids" = I(list( "67505836", "26508693", c("SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"), "31646" )), "access_time" = c( as.POSIXct("2017-01-20T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-21T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-22T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-23T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) platform <- "Seven Bridges Platform" pipeline_meta <- data.frame( "step_number" = c("1"), "name" = c("HIVE-hexagon"), "description" = c("Alignment of reads to a set of references"), "version" = c("1.3"), stringsAsFactors = FALSE ) pipeline_prerequisite <- data.frame( "step_number" = rep("1", 5), "name" = c( "Hepatitis C virus genotype 1", "Hepatitis C virus type 1b complete genome", "Hepatitis C virus (isolate JFH-1) genomic RNA", "Hepatitis C virus clone J8CF, complete genome", "Hepatitis C virus S52 polyprotein gene" ), "uri" = c( "https://www.ncbi.nlm.nih.gov/nuccore/22129792", "https://www.ncbi.nlm.nih.gov/nuccore/5420376", "https://www.ncbi.nlm.nih.gov/nuccore/13122261", "https://www.ncbi.nlm.nih.gov/nuccore/386646758", "https://www.ncbi.nlm.nih.gov/nuccore/295311559" ), "access_time" = c( as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) pipeline_input <- data.frame( "step_number" = rep("1", 2), "uri" = c( "https://example.com/dna.cgi?cmd=objFile&ids=514683", "https://example.com/dna.cgi?cmd=objFile&ids=514682" ), "access_time" = c( as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) pipeline_output <- data.frame( "step_number" = rep("1", 2), "uri" = c( "https://example.com/data/514769/allCount-aligned.csv", "https://example.com/data/514801/SNPProfile*.csv" ), "access_time" = c( as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) compose_description( keywords, xref, platform, pipeline_meta, pipeline_prerequisite, pipeline_input, pipeline_output ) %>% convert_json()
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