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Differential expression results checkpoint (SLE vs Ctrl by cell type)

Source: R/de_results.R
de_results.Rd

DESeq2 results of the comparison between SLE patients and healthy controls within each cell type, generated in the lesson "Genes diferencialmente expresados entre pacientes y controles" (l3_DEGs_es). Starting point of the functional enrichment lesson.

Usage

de_results

Format

A named list with three data frames (monocyte, moDC, tolDC), each with 21,718 rows (genes) and 7 columns:

gene

Gene symbol.

baseMean

Mean normalized expression across samples.

log2FoldChange

Log2 fold change, SLE vs Ctrl.

lfcSE

Standard error of the log2 fold change.

stat

Wald statistic.

pvalue

Wald test p-value.

padj

Benjamini-Hochberg adjusted p-value (NA for genes removed by independent filtering).

Source

Generated from filtered_txi and metadata_cleaned.

Details

For each cell type: DESeqDataSetFromTximport() with all genes of filtered_txi, design ~ Group (reference Ctrl), DESeq() and results(name = "Group_SLE_vs_Ctrl") (Wald test, Benjamini-Hochberg adjustment).

With |log2FoldChange| >= 1 and padj < 0.05: 37 up / 0 down in monocytes, 4 up / 40 down in moDC and 4 up / 12 down in tolDC (94 distinct genes). The script that generates it is data-raw/lesson3_checkpoints.R.

Examples

names(de_results)
#> [1] "monocyte" "moDC"     "tolDC"   
head(de_results$monocyte[order(de_results$monocyte$padj), ])
#>          gene  baseMean log2FoldChange     lfcSE     stat       pvalue
#> 7341    IFI27  745.8090       6.505656 0.9658170 6.735910 1.629076e-11
#> 13612    OTOF  725.5703       5.089491 0.8190471 6.213918 5.167965e-10
#> 16938 SIGLEC1 8360.4454       3.110930 0.5216396 5.963754 2.465075e-09
#> 20398   USP18  758.4596       3.123161 0.5411373 5.771475 7.858055e-09
#> 6301     GMPR  403.5613       1.645094 0.3014701 5.456907 4.844996e-08
#> 7347   IFI44L 6547.0501       2.824219 0.5508756 5.126783 2.947351e-07
#>               padj
#> 7341  1.137584e-07
#> 13612 1.804395e-06
#> 16938 5.737873e-06
#> 20398 1.371820e-05
#> 6301  6.766521e-05
#> 7347  2.725426e-04