Document metadata
Closed this issue · 1 comments
shntnu commented
metadata %>%
group_by(Metadata_dataset) %>%
skimr::skim() %>%
arrange(Metadata_dataset) %>%
filter(between(complete_rate, 0.05, 1)) %>%
group_by(skim_variable) %>%
summarise(n_datasets = n(), datasets = paste0(Metadata_dataset, collapse = ",")) %>%
arrange(desc(n_datasets), datasets) %>%
mutate(desc = "", .before = "datasets") %>%
knitr::kable()| skim_variable | n_datasets | desc | datasets |
|---|---|---|---|
| Metadata_Assay_Plate_Barcode | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_broad_sample | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_broad_sample_type | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_cell_id | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_pert_mfc_id | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_pert_type | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_pert_well | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_Plate | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_Plate_Map_Name | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_Well | 5 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_moa | 4 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1,TA-ORF-BBBC037-Rohban | |
| Metadata_well_position | 4 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_mmoles_per_liter | 3 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1 | |
| Metadata_pert_id | 3 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1 | |
| Metadata_pert_vehicle | 3 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1 | |
| Metadata_solvent | 3 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,LINCS-Pilot1 | |
| Metadata_ASSAY_WELL_ROLE | 3 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray,TA-ORF-BBBC037-Rohban | |
| Metadata_mmoles_per_liter2 | 2 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray | |
| Metadata_Sample_Dose | 2 | CDRP-BBBC047-Bray,CDRPBIO-BBBC036-Bray | |
| Metadata_target | 2 | CDRPBIO-BBBC036-Bray,LINCS-Pilot1 | |
| Metadata_pert_name | 2 | LUAD-BBBC041-Caicedo,TA-ORF-BBBC037-Rohban | |
| Metadata_pert_iname | 1 | CDRPBIO-BBBC036-Bray | |
| Metadata_pert_iname2 | 1 | CDRPBIO-BBBC036-Bray | |
| Metadata_Batch_Date | 1 | LINCS-Pilot1 | |
| Metadata_Batch_Number | 1 | LINCS-Pilot1 | |
| Metadata_broad_date | 1 | LINCS-Pilot1 | |
| Metadata_broad_id | 1 | LINCS-Pilot1 | |
| Metadata_dose_recode | 1 | LINCS-Pilot1 | |
| Metadata_InChIKey14 | 1 | LINCS-Pilot1 | |
| Metadata_mg_per_ml | 1 | LINCS-Pilot1 | |
| Metadata_pert_id_dose | 1 | LINCS-Pilot1 | |
| Metadata_plate_map_name | 1 | LINCS-Pilot1 | |
| Metadata_NCBIGeneID | 1 | LUAD-BBBC041-Caicedo | |
| Metadata_PublicID | 1 | LUAD-BBBC041-Caicedo | |
| Metadata_Transcript | 1 | LUAD-BBBC041-Caicedo | |
| Metadata_VirusPlateName | 1 | LUAD-BBBC041-Caicedo | |
| Metadata_x_mutation_status | 1 | LUAD-BBBC041-Caicedo | |
| Metadata_cell_line | 1 | TA-ORF-BBBC037-Rohban | |
| Metadata_gene_name | 1 | TA-ORF-BBBC037-Rohban | |
| Metadata_GeneID | 1 | TA-ORF-BBBC037-Rohban | |
| Metadata_Treatment | 1 | TA-ORF-BBBC037-Rohban |