plot_strand_bias {MutationalPatterns} | R Documentation

## Plot strand bias per base substitution type per group

### Description

Plot strand bias per base substitution type per group

### Usage

    plot_strand_bias(strand_bias, colors = NA, sig_type = c("fdr", "p"))

### Arguments

`strand_bias` | data.frame, result from strand_bias function
`colors` | Optional color vector with 6 values for plotting
`sig_type` | The type of significance to be used. Possible values: * 'fdr' False discovery rate. A type of multiple testing correction.; * 'p' for regular p values.

### Value

Barplot

### See Also

`mut_matrix_stranded`, `strand_occurrences`, `strand_bias_test` `plot_strand`

### Examples

    ## See the 'mut_matrix_stranded()' example for how we obtained the
    ## following mutation matrix.
    mut_mat_s <- readRDS(system.file("states/mut_mat_s_data.rds",
      package = "MutationalPatterns"
    ))

    tissue <- c(
      "colon", "colon", "colon",
      "intestine", "intestine", "intestine",
      "liver", "liver", "liver"
    )

    ## Perform the strand bias test.
    strand_counts <- strand_occurrences(mut_mat_s, by = tissue)
    strand_bias <- strand_bias_test(strand_counts)

    ## Plot the strand bias.
    plot_strand_bias(strand_bias)

    ## Use multiple (max 3) significance cutoffs.
    ## This will vary the number of significance stars.
    strand_bias_multistars <- strand_bias_test(strand_counts,
      p_cutoffs = c(0.05, 0.01, 0.005),
      fdr_cutoffs = c(0.1, 0.05, 0.01)
    )
    plot_strand_bias(strand_bias_multistars)

[Package MutationalPatterns version 3.0.1 Index]