roadmap/00.generate_txdb.R
In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data
library(GenomicFeatures)
library(GetoptLong)
library(epik)
library(epik.cmd)
PROJECT_DIR = "/icgc/dkfzlsdf/analysis/B080/guz/epik_roadmap/"
initialize_project_directory(PROJECT_DIR)
GTF_FILE = qq("@{PROJECT_DIR}/data/gen10.long.gtf")
g19 = qq("@{PROJECT_DIR}/data/gencode.v19.annotation.gtf")
txdb = match_by_gencode(GTF_FILE, g19, transcript_type == "protein_coding")
saveDb(txdb, file = qq("@{PROJECT_DIR}/txdb/gen10_long_protein_coding_gene_adjusted.sqlite"))
jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.
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library(GenomicFeatures)
library(GetoptLong)
library(epik)
library(epik.cmd)
PROJECT_DIR = "/icgc/dkfzlsdf/analysis/B080/guz/epik_roadmap/"
initialize_project_directory(PROJECT_DIR)
GTF_FILE = qq("@{PROJECT_DIR}/data/gen10.long.gtf")
g19 = qq("@{PROJECT_DIR}/data/gencode.v19.annotation.gtf")
txdb = match_by_gencode(GTF_FILE, g19, transcript_type == "protein_coding")
saveDb(txdb, file = qq("@{PROJECT_DIR}/txdb/gen10_long_protein_coding_gene_adjusted.sqlite"))
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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