Package: gDRimport 1.5.2

Arkadiusz Gladki

gDRimport: Package for handling the import of dose-response data

The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.

Authors:Arkadiusz Gladki [aut, cre], Bartosz Czech [aut], Marc Hafner [aut], Sergiu Mocanu [aut], Dariusz Scigocki [aut], Allison Vuong [aut], Luca Gerosa [aut], Janina Smola [aut]

gDRimport_1.5.2.tar.gz
gDRimport_1.5.2.zip(r-4.5)gDRimport_1.5.2.zip(r-4.4)gDRimport_1.5.2.zip(r-4.3)
gDRimport_1.5.2.tgz(r-4.4-any)gDRimport_1.5.2.tgz(r-4.3-any)
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gDRimport.pdf |gDRimport.html✨
gDRimport/json (API)
NEWS

# Install 'gDRimport' in R:

install.packages('gDRimport', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gdrplatform/gdrimport/issues

On BioConductor:gDRimport-1.5.0(bioc 3.21)gDRimport-1.4.0(bioc 3.20)

software infrastructure dataimport

7.16 score 2 stars 1 packages 5 scripts 142 downloads 26 exports 198 dependencies

Last updated 14 days agofrom:2bd8fbcb00. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 08 2024
R-4.5-win	WARNING	Nov 08 2024
R-4.5-linux	WARNING	Nov 08 2024
R-4.4-win	WARNING	Nov 08 2024
R-4.4-mac	WARNING	Nov 08 2024
R-4.3-win	WARNING	Nov 08 2024
R-4.3-mac	WARNING	Nov 08 2024

Exports:check_metadata_names convert_LEVEL5_prism_to_gDR_input convert_LEVEL6_prism_to_gDR_input convert_MAE_to_PSet convert_pset_to_df detect_file_format get_exception_data get_test_D300_data get_test_data get_test_EnVision_data get_test_Tecan_data get_test_tsv_data getPSet import_D300 is_readable_v load_data load_manifest load_results load_templates manifest_path parse_D300_xml read_excel_to_dt result_path setEnvForPSet standardize_record_values template_path

Dependencies:abind askpass assertthat backports base64enc bench BH Biobase BiocBaseUtils BiocGenerics BiocParallel bit bit64 bitops boot broom bslib BumpyMatrix cachem car carData caTools celestial cellranger checkmate cli clipr cluster codetools colorspace commonmark coop CoreGx cowplot cpp11 crayon crosstalk curl data.table DelayedArray Deriv digest doBy downloader dplyr drc DT evaluate fansi farver fastmap fastmatch fgsea fontawesome forcats foreign formatR Formula fs futile.logger futile.options gDRutils generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gplots gtable gtools haven highr hms htmltools htmlwidgets httpuv httr igraph IRanges isoband jquerylib jsonlite jsonvalidate KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle limma lme4 lsa magicaxis magrittr mapproj maps marray MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr multcomp MultiAssayExperiment munsell mvtnorm NISTunits nlme nloptr nnet numDeriv openssl openxlsx pbkrtest PharmacoGx piano pillar pkgconfig plotrix plyr pracma prettyunits profmem progress promises purrr quantreg R.methodsS3 R.oo R.utils R6 RANN rappdirs RColorBrewer Rcpp RcppEigen readr readxl relations rematch reshape2 rio rlang rmarkdown S4Arrays S4Vectors sandwich sass scales sets shiny shinydashboard shinyjs slam sm snow SnowballC sourcetools SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys TH.data tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 V8 vctrs viridisLite visNetwork vroom withr writexl xfun XML xtable XVector yaml zip zlibbioc zoo

Converting a gDR-generated MultiAssayExperiment object into a PharmacoSet

Jermiah Joseph, Bartosz Czech

Rendered fromConvertingMAEtoPharmacoSet.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-02-20
Started: 2023-10-02

Converting PharmacoSet Drug Response Data into gDR object

Jermiah Joseph, Bartosz Czech

Rendered fromConvertingPharmacoSetToGDR.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-03-14
Started: 2023-06-02

gDRimport

gDR team

Rendered fromgDRimport.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-05-22
Started: 2023-03-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Evaluate if template file with single sheet is present, if the name of the sheet is correct and if it can be fixed	.check_against_single_template_sheet
are template sheet valid?	are_template_sheets_valid
Check metadata against spaces	check_metadata_against_spaces
Check metadata field names	check_metadata_field_names
Check whether metadata headers are correct and make fixes if needed	check_metadata_headers
check_metadata_names	check_metadata_names
Check metadata for required column names	check_metadata_req_col_names
Load, convert and process the level 5 PRISM data into a gDR input	convert_LEVEL5_prism_to_gDR_input
Load, convert and process the level 6 PRISM data into a gDR input	convert_LEVEL6_prism_to_gDR_input
Convert MultiAssayExperiment to TreatmentResponseExperiment	convert_MAE_to_PSet
Convert a PharmacoSet to a data.table that is prepare for input into gDR pipeline	convert_pset_to_df
Correct names of the template sheets (if required)	correct_template_sheets
Detect format of results data	detect_file_format
Enhance raw edited EnVision data.table	enhance_raw_edited_EnVision_df
Fix typos using reference data	fix_typos_with_reference
gDR Test Data object	gdr_test_data-class
Get final results (as a data.table) from raw edited EnVision data.table	get_df_from_raw_edited_EnVision_df
Get final results (as a data.table) from raw unedited EnVision data.table	get_df_from_raw_unedited_EnVision_df
Get properties of EnVision data	get_EnVision_properties
get Excel sheets names for a charvec of files for non-Excel files return 0	get_excel_sheet_names
get exception data	get_exception_data
Get names of the sheets expected in templates xlsx	get_expected_template_sheets
Get plate info from template xlsx	get_plate_info_from_template_xlsx
get test D300 data	get_test_D300_data
get primary test data	get_test_data
get test EnVision data	get_test_EnVision_data
get test Tecan data	get_test_Tecan_data
get test tsv data	get_test_tsv_data
Get Excel sheets	get_xl_sheets
Get PharmacoSet	getPSet
Import D300	import_D300
is_readable_v Check if all paths in vector are readable	is_readable_v
Load data	load_data
Load manifest	load_manifest
Load results	load_results
Load EnVision results from xlsx	load_results_EnVision
Load tecan results from xlsx	load_results_Tecan
Load results from tsv	load_results_tsv
Load templates	load_templates
Load templates from tsv	load_templates_tsv
Load templates from xlsx	load_templates_xlsx
Method manifest_path	manifest_path manifest_path,gdr_test_data-method
grep wrapper to support multiple patterns	mgrepl
Parse D300	parse_D300_xml
Read EnVision delimited text files	read_EnVision_delim
Read in single xlsx data from EnVision	read_EnVision_xlsx
Read excel file and transorm it into data.table object	read_excel_to_dt
Read EnVision file	read_in_EnVision_file
read manifest files	read_in_manifest_file
Read in results files	read_in_result_files
read in Tecan data	read_in_results_Tecan
Read in data from xlsx template sheet	read_in_template_sheet_xlsx
Read in xlsx template files	read_in_template_xlsx
read in tsv template files	read_in_tsv_template_files
read_ref_data	read_ref_data
Method result_path	result_path result_path,gdr_test_data-method
for each drug create a Gnumber and Concentration information for each well	save_drug_info_per_well
Adjust environment variables to meet gDR standards	setEnvForPSet
standardize_record_values	standardize_record_values
Method template_path	template_path template_path,gdr_test_data-method
Validate template xlsx data	validate_template_xlsx