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Package Specifications

Specs for fastReseg_flag_all_errors:

  • Returns a genes x clusters matrix of cluster-specific reference profiles used in resegmenation pipeline. -- test: test_pipeline_wrappers.R#L54
  • Returns a list of two matrices in cluster x percentile format for the cluster-specific percentile distribution of per cell value; span_score is for the average per molecule transcript tLLR score of each cell, span_transNum is for the transcript number of each cell. -- test: test_pipeline_wrappers.R#L55 -- test: test_pipeline_wrappers.R#L68
  • Returns a data.frame for spatial modeling statistics of each cell for all cells in the data set. -- test: test_pipeline_wrappers.R#L56
  • Returns a list with each element to be a vector of UMI_cellID for cells flagged for potential cell segmentation errors within each FOV. -- test: test_pipeline_wrappers.R#L57 -- test: test_pipeline_wrappers.R#L70
  • If run with return_trimmed_perCell = TRUE,
    • Returns a gene x cell count sparse matrix where all putative contaminating transcripts are trimmed. -- test: test_pipeline_wrappers.R#L58 -- test: test_pipeline_wrappers.R#L65
  • If run with transDF_export_option =1,
    • Saves each of the per FOV outputs as individual files in path_to_output directory; flagged_transDF, modStats_ToFlagCells and classDF_ToFlagTrans would be saved as csv file, respectively. -- test: test_pipeline_wrappers.R#L72-79
    • The saved flagged_transDF csv file should be a transcript data.frame with columns for unique IDs of transcripts UMI_transID and cells UMI_cellID, for global coordinate system x, y, z, and for the goodness-of-fit in original cell segment SMI_class. -- test: test_pipeline_wrappers.R#L82

Specs for fastReseg_full_pipeline:

  • Returns a genes x clusters matrix of cluster-specific reference profiles used in resegmenation pipeline -- test: test_pipeline_wrappers.R#L129
  • Returns a list of two matrices in cluster x percentile format for the cluster-specific percentile distribution of per cell value; span_score is for the average per molecule transcript tLLR score of each cell, span_transNum is for the transcript number of each cell. -- test: test_pipeline_wrappers.R#L130 -- test: test_pipeline_wrappers.R#L145
  • Returns a list of cutoffs used in resegmentation pipeline, including, score_baseline, lowerCutoff_transNum, higherCutoff_transNum, cellular_distance_cutoff, molecular_distance_cutoff. -- test: test_pipeline_wrappers.R#L131 -- test: test_pipeline_wrappers.R#L146
  • If run with return_perCellData = TRUE,
    • Returns a per cell data.table with mean spatial coordinates, new cell type and resegmentation action after resegmentation. -- test: test_pipeline_wrappers.R#L133 -- test: test_pipeline_wrappers.R#L141
    • Returns a gene x cell count sparse matrix for updated transcript data.frame after resegmentation. -- test: test_pipeline_wrappers.R#L134 -- test: test_pipeline_wrappers.R#L142
  • If run with save_intermediates = TRUE,
    • Returns a list of 4 elements describing how the resegmenation would be performed on original transcript data.frame. -- test: test_pipeline_wrappers.R#L132 -- test: test_pipeline_wrappers.R#L147
    • Saves all intermediate files and resegmenation outputs of each FOV as single .rds object per FOV. -- test: test_pipeline_wrappers.R#L154-157
  • If run with save_intermediates = TRUE and transDF_export_option =1,
    • Saves each of the per FOV outputs as individual files with columns for resegmented outcomes, e.g. updated_cellID and updated_celltype. -- test: test_pipeline_wrappers.R#L155 -- test: test_pipeline_wrappers.R#L160

Specs for runPreprocess:

  • Runs without error when using counts, refProfiles as input but no clust. -- test: test_runPreprocess.R#L22-49
  • Runs without error when using counts, clust as input but no refProfiles. -- test: test_runPreprocess.R#L86-113
  • Runs without error when using transcript data.frame directly as input along with counts, refProfiles but no clust. -- test: test_runPreprocess.R#L151-178
  • For all input combinations,
    • Returns a vector of cluster assignments for each cell. -- test: test_runPreprocess.R#L54 -- test: test_runPreprocess.R#L123 -- test: test_runPreprocess.R#L190
    • Returns a genes x clusters matrix of cluster-specific reference profiles used in resegmenation pipeline. -- test: test_runPreprocess.R#L55 -- test: test_runPreprocess.R#L124 -- test: test_runPreprocess.R#L144 -- test: test_runPreprocess.R#L191
    • Returns a list of two matrices in cluster x percentile format for the cluster-specific percentile distribution of per cell value; span_score is for the average per molecule transcript tLLR score of each cell, span_transNum is for the transcript number of each cell. -- test: test_runPreprocess.R#L56 -- test: test_runPreprocess.R#L71 -- test: test_runPreprocess.R#L125 -- test: test_runPreprocess.R#L140 -- test: test_runPreprocess.R#L192
    • Returns a list of cutoffs used in resegmentation pipeline, including, score_baseline, lowerCutoff_transNum, higherCutoff_transNum, cellular_distance_cutoff, molecular_distance_cutoff. -- test: test_runPreprocess.R#L57 -- test: test_runPreprocess.R#L72 -- test: test_runPreprocess.R#L126 -- test: test_runPreprocess.R#L141 -- test: test_runPreprocess.R#L193-194 -- test: test_runPreprocess.R#L208-209
    • Returns a gene x cell-type score matrix to use in resegmenation pipeline. -- test: test_runPreprocess.R#L58 -- test: test_runPreprocess.R#L127
    • Returns a list of 2 elements for the intracellular and extracellular transcript data.frame of the processed outcomes of 1st transcrip file. -- test: test_runPreprocess.R#L75-83 -- test: test_runPreprocess.R#L196-203

Specs for fastReseg_perFOV_full_process:

  • Returns a updated transcript data.farme with updated_cellID and updated_celltype columns. -- test: test_perFOV_processing.R#L57 -- test: test_perFOV_processing.R#L71
  • If run with return_perCellData = TRUE,
    • Returns a per cell data.table with mean spatial coordinates, new cell type and resegmentation action after resegmentation. -- test: test_perFOV_processing.R#L58 -- test: test_perFOV_processing.R#L67
    • Returns a gene x cell count sparse matrix for the updated transcript data.frame after resegmentation. -- test: test_perFOV_processing.R#L59 -- test: test_perFOV_processing.R#L68
  • If run with return_intermediates = TRUE,
    • Returns a data.frame for spatial modeling statistics of each cell. -- test: test_perFOV_processing.R#L53 -- test: test_perFOV_processing.R#L72
    • Returns a data.frame for the group assignment of transcripts within putative wrongly segmented cells. -- test: test_perFOV_processing.R#L54 -- test: test_perFOV_processing.R#L73
    • Returns a data.frame for neighborhood environment of low-score transcript groups. -- test: test_perFOV_processing.R#L55 -- test: test_perFOV_processing.R#L74
    • Returns a list of 4 elements describing how the resegmenation would be performed on original transcript data.frame. -- test: test_perFOV_processing.R#L56 -- test: test_perFOV_processing.R#L75

Specs for runSegErrorEvaluation:

  • Returns a data.frame contains evaluation model statistics in columns for each cell's potential to have segmentation error. -- test: test_perFOV_processing.R#L102-103 -- test: test_perFOV_processing.R#L109
  • Returns a transcript data.frame with 2 additional columns: tLLR_maxCellType for cell types of maxmium transcript score under current segments and score_tLLR_maxCellType for the corresponding transcript score for each transcript. -- test: test_perFOV_processing.R#L102-106

Specs for runTranscriptErrorDetection:

  • Runs without error when using dbscan as transcript grouping method. -- test: test_perFOV_processing.R#L115-136
  • Runs without error when using delaunay as transcript grouping method. -- test: test_perFOV_processing.R#L140-163
  • For both transcript grouping methods,
  • Returns a transcript data.frame containing information for transcript score classifications and spatial group assignments as well as new cell/group ID for downstream resegmentation. -- test: test_perFOV_processing.R#L129-136 -- test: test_perFOV_processing.R#L156-163

Specs for runSegRefinement:

  • Returns the updated transcript data.frame after resegmentation with updated_cellID and updated_celltype columns. -- test: test_perFOV_processing.R#L202 -- test: test_perFOV_processing.R#L214 -- test: test_perFOV_processing.R#L226
  • If run with return_intermediates = TRUE,
    • Returns a data.frame for neighborhood environment of low-score transcript groups. -- test: test_perFOV_processing.R#L200 -- test: test_perFOV_processing.R#L215 -- test: test_perFOV_processing.R#L222
    • Returns a list of 4 elements describing how the resegmenation would be performed on original transcript data.frame. -- test: test_perFOV_processing.R#L201 -- test: test_perFOV_processing.R#L216 -- test: test_perFOV_processing.R#L223
  • If run with return_perCellData = TRUE,
    • Returns a per cell data.table with mean spatial coordinates, new cell type and resegmentation action after resegmentation. -- test: test_perFOV_processing.R#L203 -- test: test_perFOV_processing.R#L210 -- test: test_perFOV_processing.R#L224
    • Returns a gene x cell count sparse matrix for updated transcript data.frame after resegmentation. -- test: test_perFOV_processing.R#L204 -- test: test_perFOV_processing.R#L211 -- test: test_perFOV_processing.R#L219 -- test: test_perFOV_processing.R#L225