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Get a table of differential expression expression statistics with DESeq2

Source: R/02_de_analyses.R
get_deg_list.Rd

Get a table of differential expression expression statistics with DESeq2

Usage

get_deg_list(
  se,
  coldata_column = "Generation",
  parent1 = "P1",
  parent2 = "P2",
  offspring = "F1",
  midparent = "midparent",
  lfcThreshold = 0,
  alpha = 0.01,
  ...
)

Arguments

se

A SummarizedExperiment object with a count matrix and sample metadata.

coldata_column

Character indicating the name of column in colData(se) where information on the generation are stored. Default: "Generation".

parent1

Character indicating which level of the variable coldata_column represents parent 1. Default: "P1".

parent2

Character indicating which level of the variable coldata_column represents parent 2. Default: "P2".

offspring

Character indicating which level of the variable coldata_column represents the offspring (hybrid or allopolyploid). Default: "F1"

midparent

Character indicating which level of the variable coldata_column represents the midparent value. Default: "midparent", as returned by add_midparent_expression().

lfcThreshold

Numeric indicating the log2 fold-change threshold to use to consider differentially expressed genes. Default: 0.

alpha

Numeric indicating the adjusted P-value threshold to use to consider differentially expressed genes. Default: 0.01.

...

Additional arguments to be passed to DESeq2::results().

Value

A list of data frames with DESeq2's gene-wise tests statistics for each contrast. Each data frame contains the same columns as the output of DESeq2::results(). Contrasts (list names) are:

P2_vs_P1

Parent 2 (numerator) versus parent 1 (denominator).

F1_vs_P1

Offspring (numerator) versus parent 1 (denominator).

F1_vs_P2

Offspring (numerator) versus parent 2 (denominator).

F1_vs_midparent

Offspring (numerator) versus midparent (denominator).

The data frame with gene-wise test statistics in each list element contains the following variables:

baseMean

Numeric, base mean.

log2FoldChange

Numeric, log2-transformed fold changes.

lfcSE

Numeric, standard error of the log2-transformed fold changes.

stat

Numeric, observed test statistic.

pvalue

Numeric, p-value.

padj

Numeric, P-value adjusted for multiple testing.

The list contains two additional attributes named ngenes (numeric, total number of genes), and plotdata, which is a 3-column data frame with variables "gene" (character, gene ID), "lFC_F1_vs_P1" (numeric, log2 fold change between F1 and P1), and "lFC_F1_vs_P2" (numeric, log2 fold change between F1 and P2).

Examples

data(se_chlamy)
se <- add_midparent_expression(se_chlamy)
se <- add_size_factors(se, spikein = TRUE)
#> converting counts to integer mode
deg_list <- get_deg_list(se)
#> using pre-existing size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing