Run differential expression analysis with limma for continuous variable

This function runs differential expression analysis using limma for a continuous variable. It can generate and save volcano plots.

Usage

do_limma_continuous(
  olink_data,
  metadata,
  variable,
  correct = c("Sex"),
  correct_type = c("factor"),
  wide = TRUE,
  volcano = TRUE,
  pval_lim = 0.05,
  logfc_lim = 0,
  top_up_prot = 40,
  top_down_prot = 10,
  palette = "diff_exp",
  report_nproteins = TRUE,
  user_defined_proteins = NULL,
  subtitle = NULL,
  save = FALSE
)

Arguments

olink_data: A tibble with the Olink data in wide format.
metadata: A tibble with the metadata.
variable: The variable of interest.
correct: The variables to correct the results with. Default is c("Sex").
correct_type: The type of the variables to correct the results with. Default is c("factor").
wide: If the data is in wide format. Default is TRUE.
volcano: Generate volcano plots. Default is TRUE.
pval_lim: The p-value limit for significance. Default is 0.05.
logfc_lim: The logFC limit for significance. Default is 0.
top_up_prot: The number of top up regulated proteins to label on the plot. Default is 40.
top_down_prot: The number of top down regulated proteins to label on the plot. Default is 10.
palette: The color palette for the plot. If it is a character, it should be one of the palettes from get_hpa_palettes(). Default is "diff_exp".
report_nproteins: If the number of significant proteins should be reported in the subtitle. Default is TRUE.
user_defined_proteins: A list with the user defined proteins to label on the plot. Default is NULL.
subtitle: The subtitle of the plot or NULL for no subtitle.
save: Save the volcano plots. Default is FALSE.

Value

A list with the differential expression results and volcano plots.

de_results: A list with the differential expression results.
volcano_plot: A list with the volcano plots.

Details

It will filter out rows with NA values in any of the columns that are used for correction, either the variable or in correct. The user_defined_proteins overrides the top_up_prot and top_down_prot arguments.

Examples

do_limma_continuous(example_data, example_metadata, "Age", wide = FALSE)
#> $de_results
#> # A tibble: 100 × 9
#>    Assay        logFC as.factor.Sex.F as.factor.Sex.M AveExpr     F   P.Value
#>    <chr>        <dbl>           <dbl>           <dbl>   <dbl> <dbl>     <dbl>
#>  1 ADAMTS15 -0.000719            3.09            2.92    2.99 1874. 2.10e-291
#>  2 AARSD1    0.000327            2.96            3.25    3.13 1608. 1.29e-274
#>  3 AKT1S1    0.00154             3.28            3.46    3.47 1478. 3.54e-265
#>  4 ATG4A    -0.00157             2.56            2.71    2.55 1138. 2.26e-238
#>  5 ATOX1    -0.00166             3.02            3.18    2.97 1061. 1.13e-232
#>  6 ADM       0.00536             1.53            1.47    1.87  954. 7.63e-224
#>  7 AK1      -0.00373             2.51            2.66    2.34  786. 3.94e-202
#>  8 AKR1B1   -0.000171            2.28            2.33    2.29  783. 2.64e-200
#>  9 ATP5IF1  -0.00321             3.66            4.02    3.60  740. 1.11e-196
#> 10 ARHGEF12 -0.00163             3.19            3.56    3.26  683. 2.06e-187
#> # ℹ 90 more rows
#> # ℹ 2 more variables: adj.P.Val <dbl>, sig <chr>
#> 
#> $volcano_plot

#>