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 `prepareDEG` which saved expression data and ranking data of genes
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