sc_DTU_analysis {FLAMES} | R Documentation

## FLAMES Differential Transcript Usage Analysis

### Description

Chi-square based differential transcription usage analysis. This variant is meant for single cell data. Takes the `SingleCellExperiment` object from `sc_long_pipeline` as input. Alternatively, the path to the output folder could be provided instead of the SCE object. A cluster annotation file `cluster_annotation.csv` is required, please provide this file under the output folder of `sc_long_pipeline`.

### Usage

    sc_DTU_analysis(sce, path, min_count = 15)

### Arguments

`sce` | The `SingleCellExperiment` object from `sc_long_pipeline`, an additional `cluster_annotation.csv` file is required under the output folder of the SCE object.
`path` | The path to the output folder of `sc_long_pipeline` the folder needs to contain: transcript_count.csv.gz - the transcript count matrix isoform_FSM_annotation.csv - the full splice match annotation file cluster_annotation.csv - cluster annotation file
`min_count` | The minimum UMI count threshold for filtering isoforms.

### Details

This function will search for genes that have at least two isoforms, each with more than `min_count` UMI counts. For each gene, the per cell transcript counts were merged by group to generate pseudo bulk samples. Grouping is specified by the `cluster_annotation.csv` file. The top 2 highly expressed transcripts for each group were selected and a UMI count matrix where the rows are selected transcripts and columns are groups was used as input to a chi-square test of independence (chisq.test). Adjusted P-values were calculated by Benjamini–Hochberg correction.

### Value

a `data.frame` containing the following columns:

- gene_name - differentially transcribed genes

- X_value - the X value for the DTU gene

- df - degrees of freedom of the approximate chi-squared distribution of the test statistic

- DTU_tr - the transcript_id with the highest squared residuals

- DTU_group - the cell group with the highest squared residuals

- p_value - the p-value for the test

- adj_p - the adjusted p-value (by Benjamini–Hochberg correction)

The table is sorted by decreasing P-values. It will also be saved as `sc_DTU_analysis.csv` under the output folder.

[Package FLAMES version 1.0.2 Index]