Description Usage Arguments Value Examples
View source: R/run_annotation.R
Run UTR annotation on a variant file to check whether a variant alter any of the feature element in UTRs, return a CSV file with annotated information
1 2 3 4 5 6 7 8 9 10 11 12 |
variantFile |
a CSV file with Chr, Pos, Ref, Alt |
annotationResult |
output annotation file |
species |
species, either human or mouse |
ensemblVersion |
(optional) a number specifying which version of Ensembl annotation you'd like to use, by default use the latest version |
dataDir |
(optional) path to the store / extract database information, if not specified will create a folder named as input variant file name with a "db_" prefix |
conservationBwFiles |
(optional) path to a folder which contains one or more conservation bigWig files. If not set, will skip conservation analysis. |
cores |
(optional) number of cores to use for parallel computing. If not specified, use a single core by default. |
format |
(optional) csv or vcf, the default is csv |
mrl_prediction |
(optional) Whether do MRL prediction and check if it increase or decrease. The default is TRUE. |
verbose |
Whether print diagnostic messages. The default is FALSE. |
A CSV file with annotated variants
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | test_variant_file <- system.file("extdata", "variants_sample.csv", package = "utr.annotation")
# run UTR annotation with 1 core and skip getting conservation scores for variant positions
runUTRAnnotation(variantFile = test_variant_file,
annotationResult = "annotated_variants_sample.csv",
species = "human",
ensemblVersion = 93,
dataDir = "test_db")
unlink("test_db", recursive = TRUE)
unlink("annotated_variants_sample.csv")
## Not run:
# Download BigWig format conservation track files hg38.phastCons100way.bw and hg38.phyloP100way.bw
# from UCSC Genome Browser to a folder (here we name it folder_store_conservation_bw_files)
Conservation_scores <- "folder_store_conservation_bw_files"
runUTRAnnotation(variantFile = test_variant_file,
annotationResult = "annotated_variants_sample.csv",
species = "human",
ensemblVersion = 93,
dataDir = "test_db",
cores = 8,
conservationBwFiles = Conservation_scores)
## End(Not run)
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