In tidytranscriptomics-workshops/rpharma2021_tidytranscriptomics: Introduction to Tidy Transcriptomics

What fraction of variance is explained by PC3?

counts_scal_PCA <-
  counts_tt %>%
  scale_abundance() %>%
  reduce_dimensions(method = "PCA", .dims = 3)

Which method detects the most differentially abundant transcripts, p value adjusted for multiple testing < 0.05 (FDR, adj.P.Val, padj)?

de_all %>%

  # Subset transcript information
  pivot_transcript() %>%

  # Reshape for nesting
  pivot_longer(
    cols = -c(feature, symbol, .abundant, group:exon_name),
    names_sep = "_",
    names_to = c("method", "statistic"),
    values_to = "value"
  ) %>%

  # Filter statistic
  filter(statistic %in% c("FDR", "adj.P.Val", "padj")) %>%  
  filter(value < 0.05) %>%

  # Counting
  count(method) %>%

  # Sort
  arrange(desc(n))

What is the most abundant cell type overall in BRCA samples?

BRCA_cell_type_long %>%
  group_by(cell_type) %>%
  summarise(m = median(proportion)) %>%
  dplyr::arrange(dplyr::desc(m))

Single-cell nesting - quality control

mito_info_all_datasets <- pbmc_nested %>%
    mutate(mitochondrion_info = map(
    data,
    ~ # Calculate mitochondrial statistics
      perCellQCMetrics(.x, subsets = list(Mito = which(location == "MT"))) %>%

      # Convert to tibble
      as_tibble(rownames = "cell") %>%

      # Label cells with high mitochondrial content
      mutate(high_mitochondrion = isOutlier(subsets_Mito_percent, type = "higher"))
  ))

mito_info_all_datasets

Reducing dimension - UMAP

UMAP 1 of 2 components has More variability than 3 components

left_join(
    pbmc %>%
    runUMAP(ncomponents = 2, dimred="corrected") %>% 
        as_tibble() %>% 
        select(cell, UMAP1),
    pbmc %>%
        runUMAP(ncomponents = 3, dimred="corrected") %>% 
        as_tibble() %>% 
        select(cell, UMAP1),
    by="cell"
) %>%
    summarise(sd(UMAP1.x), sd(UMAP1.y))

Cell annotation

Skeletal muscle

pbmc %>% count(label, first.labels) %>% arrange(desc(n))

tidytranscriptomics-workshops/rpharma2021_tidytranscriptomics documentation built on Dec. 23, 2021, 10:53 a.m.