Closed jaeddy closed 4 years ago
These lines in build_feature_tables.R seem to be outdated (on the feature/feather_file_structure branch here):
build_feature_tables.R
feature/feather_file_structure
cat(crayon::magenta("Importing feather file for features."), fill = TRUE) features <- read_iatlas_data_file(feather_file_folder, "/SQLite_data/features.feather") %>% dplyr::rename(name = feature) %>% dplyr::mutate(class = ifelse(is.na(class), default_class, class)) cat(crayon::blue("Imported feather file for features."), fill = TRUE)
Neither the SQLite_data/ folder nor the features.feather file seem to exist under feather_files/:
SQLite_data/
features.feather
feather_files/
feather_files/ ├── driver_results │ └── driver_results.feather ├── ecn_genes.feather ├── edges │ ├── edges_TCGAImmune.feather │ ├── edges_TCGAStudy.feather │ ├── edges_TCGAStudy_Immune.feather │ └── edges_TCGASubtype.feather ├── expr_matrix.feather ├── features │ ├── immune_subtype_features.feather │ ├── tcga_study_features.feather │ └── tcga_subtype_features.feather ├── fmx_df.feather ├── gene_ids.feather ├── genes │ ├── driver_mutation_genes.feather │ ├── extra_cellular_network_genes.feather │ ├── immunomodulator_genes.feather │ └── io_target_genes.feather ├── network_node_label_friendly.feather ├── nodes │ ├── nodes_TCGAImmune.feather │ ├── nodes_TCGAStudy.feather │ ├── nodes_TCGAStudy_Immune.feather │ └── nodes_TCGASubtype.feather ├── relationships │ ├── features_to_samples │ │ ├── immune_subtype_features_to_samples.feather │ │ ├── tcga_study_features_to_samples.feather │ │ └── tcga_subtype_features_to_samples.feather │ └── nodes_to_tags │ ├── immune_subtype_nodes_to_tags.feather │ ├── tcga_study_nodes_to_tags.feather │ └── tcga_subtype_nodes_to_tags.feather ├── samples │ ├── immune_subtype_samples.feather │ ├── immune_subtype_samples_to_tags.feather │ ├── tcga_study_samples.feather │ ├── tcga_study_samples_to_tags.feather │ ├── tcga_subtype_samples.feather │ └── tcga_subtype_samples_to_tags.feather └── tags ├── immune_subtype_tags.feather ├── tcga_study_tags.feather └── tcga_subtype_tags.feather
Those files have been committed to the repo.
These lines in
build_feature_tables.R
seem to be outdated (on thefeature/feather_file_structure
branch here):Neither the
SQLite_data/
folder nor thefeatures.feather
file seem to exist underfeather_files/
: