Barcode abundance comparison — compareAbundance • bartools

Takes a DGElist list object with counts and samples dataframe. Finds differentially abundant barcodes between two experimental conditions, using the likelihood ratio test (LRT) based on the fitted generalized linear model (GLM) to compare two nested models, typically a reduced model and a full model, to determine if the additional terms in the full model significantly improve the model fit. Additionally, it computes the p-values associated with the test statistic for each barcode. It save the results in a csv file and returns a volcano plot.

Usage

compareAbundance(
  dgeObject,
  group,
  condition1,
  condition2,
  pval = 0.05,
  logFC = 2,
  filename = NULL
)

Arguments

dgeObject: DGEList object with barcode counts.
group: Column name in sample metadata to group samples by (string).
condition1: Name of reference condition in group column (string).
condition2: Name of second condition in group column (string).
pval: Pvalue threshold for the volcano plot (decimal). Default = `0.05`.
logFC: logFC threshold for the volcano plot (decimal). Default = `2`.
filename: Optional, filename for the results of the likelihood ratio test (string).

Value

Returns a volcano plot and a csv file with differentially abundant barcode results

Details

compareAbundance

Examples

data(test.dge)
compareAbundance(test.dge, group = "Treatment", condition1 = "Vehicle", condition2 = "Low_dose")