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Differential expression results: between-group comparison of contrasts

Source: R/de_interaction_results.R
de_interaction_results.Rd

DESeq2 interaction results that test whether the change from monocytes to in vitro differentiated dendritic cells (moDC or tolDC) is different in SLE patients than in healthy controls. Used in the lesson about the between-group comparison of contrasts (l7_DEGs_between_groups_es; Figure 7A and 7B of the article).

Usage

de_interaction_results

Format

A named list with two data frames (moDC and tolDC), each with 21,718 rows (genes) and 7 columns: gene, baseMean, log2FoldChange, lfcSE, stat, pvalue and padj (see de_results).

Source

Generated from filtered_txi and metadata_cleaned.

Details

Design (all genes of filtered_txi, the 99 samples, reference levels Ctrl and monocyte): ~ Group + Cell_type + Group:Cell_type. Results were extracted with results(alpha = 0.05, name = "GroupSLE.Cell_type<moDC|tolDC>") (Wald test, Benjamini-Hochberg adjustment). The log2FoldChange is a difference of differences: (dendritic cell vs monocyte in SLE) minus (dendritic cell vs monocyte in Ctrl).

With padj < 0.05 (up / down): moDC 1 / 28 and tolDC 3 / 38. The script that generates this object is data-raw/lesson7_checkpoints.R.

See also

de_celltype_results (dendritic cells vs monocytes within each group), go_interaction_results.

Examples

names(de_interaction_results)
#> [1] "moDC"  "tolDC"
head(de_interaction_results$tolDC[order(de_interaction_results$tolDC$padj), ])
#>         gene   baseMean log2FoldChange     lfcSE      stat       pvalue
#> 7705   ISG15 1571.72540     -2.3242527 0.3964015 -5.863381 4.535367e-09
#> 7348    IFI6 5171.46042     -2.1636287 0.4035187 -5.361905 8.234902e-08
#> 7345   IFI35 1270.40241     -1.1028139 0.2149937 -5.129518 2.904851e-07
#> 1690    BST2 6388.65236     -0.8485252 0.1706817 -4.971388 6.647534e-07
#> 16889 SH3TC2   18.24524     -4.6162394 0.9279896 -4.974452 6.543263e-07
#> 5079    ETV7   57.87252     -3.7694878 0.7671254 -4.913783 8.933559e-07
#>               padj
#> 7705  6.634789e-05
#> 7348  6.023419e-04
#> 7345  1.416502e-03
#> 1690  1.944936e-03
#> 16889 1.944936e-03
#> 5079  2.178151e-03