This function returns a dataframe having first column gene names and subsequent columns are
fold change values for the comparisons passed through sample_comparisons.
Arguments
- x
an abject of class "parcutils". This is an output of the function
run_deseq_analysis().- sample_comparisons
a character vector denoting sample comparisons for which fold change values to be derived.
- genes
a character vector denoting gene names for which fold change values to be derived.
Examples
count_file <- system.file("extdata","toy_counts.txt" , package = "parcutils")
count_data <- readr::read_delim(count_file, delim = "\t")
#> Rows: 5000 Columns: 10
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (1): gene_id
#> dbl (9): control_rep1, control_rep2, control_rep3, treat1_rep1, treat1_rep2,...
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
sample_info <- count_data %>% colnames() %>% .[-1] %>%
tibble::tibble(samples = . , groups = rep(c("control" ,"treatment1" , "treatment2"), each = 3) )
res <- run_deseq_analysis(counts = count_data ,
sample_info = sample_info,
column_geneid = "gene_id" ,
group_numerator = c("treatment1", "treatment2") ,
group_denominator = c("control"))
#> ℹ Running DESeq2 ...
#> converting counts to integer mode
#> Warning: some variables in design formula are characters, converting to factors
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
#> ✔ Done.
#> ℹ Summarizing DEG ...
#> ✔ Done.
genes = parcutils::get_genes_by_regulation(x = res, sample_comparison = "treatment2_VS_control") %>% names()
fc_df <- get_fold_change_matrix(x = res, sample_comparison = c("treatment2_VS_control" , "treatment1_VS_control"), genes = genes)
print(fc_df)
#> # A tibble: 835 × 3
#> gene_id treatment1_VS_control treatment2_VS_control
#> <chr> <dbl> <dbl>
#> 1 ENSG00000139263:LRIG3 -0.138 -1.18
#> 2 ENSG00000072135:PTPN18 -0.589 -1.93
#> 3 ENSG00000204531:POU5F1 -0.155 -1.06
#> 4 ENSG00000144840:RABL3 -0.157 -1.76
#> 5 ENSG00000178597:PSAPL1 -0.191 -1.68
#> 6 ENSG00000186472:PCLO -0.687 -2.17
#> 7 ENSG00000155918:RAET1L 0.467 2.63
#> 8 ENSG00000151458:ANKRD50 -0.0441 1.91
#> 9 ENSG00000151623:NR3C2 -0.298 -2.83
#> 10 ENSG00000172725:CORO1B -0.400 -2.10
#> # … with 825 more rows