queryEncode {ENCODExplorer} | R Documentation |
After running the prepare_ENCODEDb
function, this function will allow
you to extract a subset of data encording to the following criteria :
accession, assay name, biosample, dataset accession, file accession,
file format, laboratory, donor organism, target and treatment.
queryEncode(df = get_encode_df(), set_accession = NULL, assay = NULL, biosample_name = NULL, dataset_accession = NULL, file_accession = NULL, file_format = NULL, lab = NULL, organism = NULL, target = NULL, treatment = NULL, project = NULL, biosample_type = NULL, file_status = "released", status = "released", fixed = TRUE, quiet = FALSE, fuzzy = FALSE)
df |
|
set_accession |
character string to select the accession |
assay |
character string to select the assay type |
biosample_name |
character string to select the biosample name |
dataset_accession |
character string to select the dataset accession |
file_accession |
character string to select the file accesion |
file_format |
character string to select the file format |
lab |
character string to select the laboratory |
organism |
character string to select the donor organism |
target |
character string to select the experimental target |
treatment |
character string to select the treatment |
project |
character string to select the project |
biosample_type |
character string to select the biosample type |
file_status |
character string to select the file status ("released", "revoked", "all"). Default "released" |
status |
character string to select the dataset/experiment status |
fixed |
logical. If TRUE, pattern is a string to be matched as it is. |
quiet |
logical enables to switch off the result summary information when setting at TRUE. |
fuzzy |
Search for substring or alternate hyphenations. Default: TRUE |
By default, the query can be made on an exact match term. This behaviour can
be modified by setting the fixed
argument at TRUE
a data.frame
s containing data about ENCODE
experiments and datasets
queryEncode(df = get_encode_df_demo(), biosample_name = "A549", file_format = "bam")