rworkflows
.get_data()
--> echodata
get_os()
--> echodata
load_rdata()
--> downloadR
example_sumstats_paths()
--> echpdata::get_Nalls2019_loci()
find_consensus_SNPs
--> echodata::find_consensus_snps()
locus_plot
--> echoplot
eQTLcatalogue_
.COLOC_
.gwas_data
--> query_granges
genome_build
--> query_genome
echotabix::construct_query()
gwas.data
, chrom
, bp_min
, bp_max
COLOC_heatmap
COLOC_corplot
meta
data to include latest paths and datasets.fix_ftp
: Replacing "ftp:" prefix with "http:" seems to drastically improve the
ability of functions to query the files. NEWS.md
file to track changes to the package.data.table
version requirement
(issues with compressed files have since been resolved).biocthis::use_bioc_github_action(pkgdown_covr_branch = c("main","master"))
. T
/F
with TRUE
/FALSE
in accordance with best coding practices.echotabix
echoconda
echodata
datasets:BST1
LRRK2
MEX3C
styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
printer
with messager
. eQTL_Catalogue.list_datasets
. get_coloc_QTLs
: coloc_QTLs_full
to Releases as it was >12Mb. coloc_QTLs
to Releases as it was >1.5Mb. example_eQTL_Catalogue_query_paths
. echotabix::liftover
(removed unused deps). rsids_from_coords
with echodata::coords_to_rsids
(removed unused deps). method
for all relevant functions.gather_files
in favor of more descriptive merge_files
gather_colocalized_data
in favor of more descriptive
merge_colocalized_data
library
calls within functions. requireNamespace
where suggests are used.eQTL_Catalogue.query
so that the default is use_tabix=FALSE
due to
instability of using tabix
with the EBI server. See here for details. run_coloc
automatically infers (effective) sample size and checks that MAF
is present for all SNPs (after removing MAF>=1 or <=0 or ==NA).MEX3C__Alasoo_2018.macrophage_IFNg
)
from built-in data as these were already included in exdata.First version of catalogueR
created as a sister package of echolocatoR
.
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