transcriptome {fastcpd}

Transcription Profiling of 57 Human Bladder Carcinoma Samples

Description

Transcriptome analysis of 57 bladder carcinomas on Affymetrix HG-U95A and HG-U95Av2 microarrays

Usage

transcriptome

Format

A data frame with 2215 rows and 43 variables:

3

Individual 3

4

Individual 4

5

Individual 5

6

Individual 6

7

Individual 7

8

Individual 8

9

Individual 9

10

Individual 10

14

Individual 14

15

Individual 15

16

Individual 16

17

Individual 17

18

Individual 18

19

Individual 19

21

Individual 21

22

Individual 22

24

Individual 24

26

Individual 26

28

Individual 28

30

Individual 30

31

Individual 31

33

Individual 33

34

Individual 34

35

Individual 35

36

Individual 36

37

Individual 37

38

Individual 38

39

Individual 39

40

Individual 40

41

Individual 41

42

Individual 42

43

Individual 43

44

Individual 44

45

Individual 45

46

Individual 46

47

Individual 47

48

Individual 48

49

Individual 49

50

Individual 50

51

Individual 51

53

Individual 53

54

Individual 54

57

Individual 57

Source

<https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-TABM-147>

<https://github.com/cran/ecp/tree/master/data>

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  result <- fastcpd.mean(transcriptome$"10", trim = 0.005)
  summary(result)
  plot(result)

  result_all <- fastcpd.mean(
    transcriptome,
    beta = (ncol(transcriptome) + 1) * log(nrow(transcriptome)) / 2 * 5,
    trim = 0
  )

  plots <- lapply(
    seq_len(ncol(transcriptome)), function(i) {
      ggplot2::ggplot(
        data = data.frame(
          x = seq_along(transcriptome[, i]), y = transcriptome[, i]
        ),
        ggplot2::aes(x = x, y = y)
      ) +
        ggplot2::geom_line(color = "steelblue") +
        ggplot2::geom_vline(
          xintercept = result_all@cp_set,
          color = "red",
          linetype = "dotted",
          linewidth = 0.5,
          alpha = 0.7
        ) +
        ggplot2::theme_void()
    }
  )

  if (requireNamespace("gridExtra", quietly = TRUE)) {
    gridExtra::grid.arrange(grobs = plots, ncol = 1, nrow = ncol(transcriptome))
  }
}