This utility function allows quick text-based search of available
fields for using grep
Arguments
- entity
one of the available gdc entities ('files','cases',...) against which to gather available fields for matching
- pattern
A regular expression that will be used in a call to
grep- ...
passed on to grep
- value
logical(1) whether to return values as opposed to indices (passed along to grep)
Examples
grep_fields('files','analysis')
#> [1] "analysis.analysis_id"
#> [2] "analysis.analysis_type"
#> [3] "analysis.created_datetime"
#> [4] "analysis.input_files.access"
#> [5] "analysis.input_files.average_base_quality"
#> [6] "analysis.input_files.average_insert_size"
#> [7] "analysis.input_files.average_read_length"
#> [8] "analysis.input_files.channel"
#> [9] "analysis.input_files.chip_id"
#> [10] "analysis.input_files.chip_position"
#> [11] "analysis.input_files.contamination"
#> [12] "analysis.input_files.contamination_error"
#> [13] "analysis.input_files.created_datetime"
#> [14] "analysis.input_files.data_category"
#> [15] "analysis.input_files.data_format"
#> [16] "analysis.input_files.data_type"
#> [17] "analysis.input_files.error_type"
#> [18] "analysis.input_files.experimental_strategy"
#> [19] "analysis.input_files.file_id"
#> [20] "analysis.input_files.file_name"
#> [21] "analysis.input_files.file_size"
#> [22] "analysis.input_files.imaging_date"
#> [23] "analysis.input_files.magnification"
#> [24] "analysis.input_files.md5sum"
#> [25] "analysis.input_files.mean_coverage"
#> [26] "analysis.input_files.msi_score"
#> [27] "analysis.input_files.msi_status"
#> [28] "analysis.input_files.pairs_on_diff_chr"
#> [29] "analysis.input_files.plate_name"
#> [30] "analysis.input_files.plate_well"
#> [31] "analysis.input_files.platform"
#> [32] "analysis.input_files.proc_internal"
#> [33] "analysis.input_files.proportion_base_mismatch"
#> [34] "analysis.input_files.proportion_coverage_10X"
#> [35] "analysis.input_files.proportion_coverage_10x"
#> [36] "analysis.input_files.proportion_coverage_30X"
#> [37] "analysis.input_files.proportion_coverage_30x"
#> [38] "analysis.input_files.proportion_reads_duplicated"
#> [39] "analysis.input_files.proportion_reads_mapped"
#> [40] "analysis.input_files.proportion_targets_no_coverage"
#> [41] "analysis.input_files.read_pair_number"
#> [42] "analysis.input_files.revision"
#> [43] "analysis.input_files.stain_type"
#> [44] "analysis.input_files.state"
#> [45] "analysis.input_files.state_comment"
#> [46] "analysis.input_files.submitter_id"
#> [47] "analysis.input_files.total_reads"
#> [48] "analysis.input_files.tumor_ploidy"
#> [49] "analysis.input_files.tumor_purity"
#> [50] "analysis.input_files.updated_datetime"
#> [51] "analysis.metadata.read_groups.RIN"
#> [52] "analysis.metadata.read_groups.adapter_name"
#> [53] "analysis.metadata.read_groups.adapter_sequence"
#> [54] "analysis.metadata.read_groups.base_caller_name"
#> [55] "analysis.metadata.read_groups.base_caller_version"
#> [56] "analysis.metadata.read_groups.chipseq_antibody"
#> [57] "analysis.metadata.read_groups.chipseq_target"
#> [58] "analysis.metadata.read_groups.created_datetime"
#> [59] "analysis.metadata.read_groups.days_to_sequencing"
#> [60] "analysis.metadata.read_groups.experiment_name"
#> [61] "analysis.metadata.read_groups.flow_cell_barcode"
#> [62] "analysis.metadata.read_groups.fragment_maximum_length"
#> [63] "analysis.metadata.read_groups.fragment_mean_length"
#> [64] "analysis.metadata.read_groups.fragment_minimum_length"
#> [65] "analysis.metadata.read_groups.fragment_standard_deviation_length"
#> [66] "analysis.metadata.read_groups.fragmentation_enzyme"
#> [67] "analysis.metadata.read_groups.includes_spike_ins"
#> [68] "analysis.metadata.read_groups.instrument_model"
#> [69] "analysis.metadata.read_groups.is_paired_end"
#> [70] "analysis.metadata.read_groups.lane_number"
#> [71] "analysis.metadata.read_groups.library_name"
#> [72] "analysis.metadata.read_groups.library_preparation_kit_catalog_number"
#> [73] "analysis.metadata.read_groups.library_preparation_kit_name"
#> [74] "analysis.metadata.read_groups.library_preparation_kit_vendor"
#> [75] "analysis.metadata.read_groups.library_preparation_kit_version"
#> [76] "analysis.metadata.read_groups.library_selection"
#> [77] "analysis.metadata.read_groups.library_strand"
#> [78] "analysis.metadata.read_groups.library_strategy"
#> [79] "analysis.metadata.read_groups.multiplex_barcode"
#> [80] "analysis.metadata.read_groups.number_expect_cells"
#> [81] "analysis.metadata.read_groups.platform"
#> [82] "analysis.metadata.read_groups.read_group_id"
#> [83] "analysis.metadata.read_groups.read_group_name"
#> [84] "analysis.metadata.read_groups.read_group_qcs.adapter_content"
#> [85] "analysis.metadata.read_groups.read_group_qcs.basic_statistics"
#> [86] "analysis.metadata.read_groups.read_group_qcs.created_datetime"
#> [87] "analysis.metadata.read_groups.read_group_qcs.encoding"
#> [88] "analysis.metadata.read_groups.read_group_qcs.fastq_name"
#> [89] "analysis.metadata.read_groups.read_group_qcs.kmer_content"
#> [90] "analysis.metadata.read_groups.read_group_qcs.overrepresented_sequences"
#> [91] "analysis.metadata.read_groups.read_group_qcs.per_base_n_content"
#> [92] "analysis.metadata.read_groups.read_group_qcs.per_base_sequence_content"
#> [93] "analysis.metadata.read_groups.read_group_qcs.per_base_sequence_quality"
#> [94] "analysis.metadata.read_groups.read_group_qcs.per_sequence_gc_content"
#> [95] "analysis.metadata.read_groups.read_group_qcs.per_sequence_quality_score"
#> [96] "analysis.metadata.read_groups.read_group_qcs.per_tile_sequence_quality"
#> [97] "analysis.metadata.read_groups.read_group_qcs.percent_gc_content"
#> [98] "analysis.metadata.read_groups.read_group_qcs.read_group_qc_id"
#> [99] "analysis.metadata.read_groups.read_group_qcs.sequence_duplication_levels"
#> [100] "analysis.metadata.read_groups.read_group_qcs.sequence_length_distribution"
#> [101] "analysis.metadata.read_groups.read_group_qcs.state"
#> [102] "analysis.metadata.read_groups.read_group_qcs.submitter_id"
#> [103] "analysis.metadata.read_groups.read_group_qcs.total_sequences"
#> [104] "analysis.metadata.read_groups.read_group_qcs.updated_datetime"
#> [105] "analysis.metadata.read_groups.read_group_qcs.workflow_end_datetime"
#> [106] "analysis.metadata.read_groups.read_group_qcs.workflow_link"
#> [107] "analysis.metadata.read_groups.read_group_qcs.workflow_start_datetime"
#> [108] "analysis.metadata.read_groups.read_group_qcs.workflow_type"
#> [109] "analysis.metadata.read_groups.read_group_qcs.workflow_version"
#> [110] "analysis.metadata.read_groups.read_length"
#> [111] "analysis.metadata.read_groups.rin"
#> [112] "analysis.metadata.read_groups.sequencing_center"
#> [113] "analysis.metadata.read_groups.sequencing_date"
#> [114] "analysis.metadata.read_groups.single_cell_library"
#> [115] "analysis.metadata.read_groups.size_selection_range"
#> [116] "analysis.metadata.read_groups.spike_ins_concentration"
#> [117] "analysis.metadata.read_groups.spike_ins_fasta"
#> [118] "analysis.metadata.read_groups.state"
#> [119] "analysis.metadata.read_groups.submitter_id"
#> [120] "analysis.metadata.read_groups.target_capture_kit"
#> [121] "analysis.metadata.read_groups.target_capture_kit_catalog_number"
#> [122] "analysis.metadata.read_groups.target_capture_kit_name"
#> [123] "analysis.metadata.read_groups.target_capture_kit_target_region"
#> [124] "analysis.metadata.read_groups.target_capture_kit_vendor"
#> [125] "analysis.metadata.read_groups.target_capture_kit_version"
#> [126] "analysis.metadata.read_groups.to_trim_adapter_sequence"
#> [127] "analysis.metadata.read_groups.updated_datetime"
#> [128] "analysis.state"
#> [129] "analysis.submitter_id"
#> [130] "analysis.updated_datetime"
#> [131] "analysis.workflow_end_datetime"
#> [132] "analysis.workflow_link"
#> [133] "analysis.workflow_start_datetime"
#> [134] "analysis.workflow_type"
#> [135] "analysis.workflow_version"
#> [136] "cases.follow_ups.molecular_tests.molecular_analysis_method"
#> [137] "downstream_analyses.analysis_id"
#> [138] "downstream_analyses.analysis_type"