Output data¶
Outputs all resulting directories, files, and figures to directory specified as the workingDir
when creating an instance of class Analysis
.
It will also output an analysis report detailing all results and figures.
Directories¶
These subdirectories are created and:
Contains a folder for each individual bootstrap experiment which includes:
Files |
Description |
---|---|
batches.txt |
List of batches used in the analysis |
comparison.xlsx |
Evolutionary conservation file |
dendrogram-heatmap-correlation-data.(h5/xlsx) |
For each gene holds all measurement data (e.g. cluster, Fraction, Top50 overlap, etc.). Contains correlation distance of expression measure. |
dendrogram-heatmap-correlation.png |
Saved dendrogram, heatmap, and bargraphs, see example below |
metricFile.h5 |
Gene expression data for specified metric |
per-gene-measures-correlation.(h5 & xlsx) |
Intra-measures from each gene |
perGeneStats.h5 |
For each gene holds fraction of cells expressing it, median expression, and per batch counts |
size.txt |
Size of input data (number of cells and genes) |
Gene expression distance is calculated for each batch, and results are not grouped, and are further used in bootstrap analysis.
Files |
Description |
---|---|
dendrogram-heatmap-correlation-data.(h5/xlsx) |
For each gene holds all measurement data (e.g. cluster, Fraction, Top50 overlap, etc.). Contains correlation distance of expression measure. |
metricsFile.h5 |
Gene expression data for specified metric |
per-gene-measures-correlation.(h5/xlsx) |
Intra-measures from each gene |
perGeneStats.h5 |
For each gene holds fraction of cells expressing it, median expression, and per batch counts |
size.txt |
Size of input data (number of cells and genes) |
Contains files saved from Scramble function
Files |
Description |
---|---|
combined_M_aligned.h5 |
Temporary file that holds distribution data; removed when analysis is completed. |
se_distribution.png |
Plotted counts distribution |
se_distribution.xlsx |
Counts distribution data |
Files¶
Files |
Description |
---|---|
bootstrap_experiments_dendro_data.h5 |
Aggregation of all gene measurement data and correlation distance of expression measure for all bootstrap experiments |
data.h5 |
Output file from |
results.png |
Saved dendrogram, heatmap, and bargraphs, see example below |
For each combination of measurements (variant) of interest each of these files are outputted:
Files |
Description |
---|---|
bootstrap_in-peak_genes_SD.xlsx |
Aggregation of all gene measurement data and correlation distance of expression measure for all bootstrap experiments |
variant.xlsx |
For each gene gives the percentage of bootstrap experiments in which it apppears in a peak along with mean, standard deviation, and covariance calculations. For each bootstrap experiment lists genes in the peak. |
variability.xlsx |
Holds mean, standard deviation, and covariance calculations |
Example of result figures using mouse PangLaoDB DCS-annotated endothelial cells