SNV: Single nucleotide variant (SNV) data from colon cancer...

In BoutrosLab.plotting.general: Functions to Create Publication-Quality Plots

Single nucleotide variant (SNV) data from colon cancer patients

Description

SNV calls from 30 genes across 58 colon cancer patients. Additional data on the patient samples is found in in the "patient" dataset. The same patient samples are described in the "microarray" and "CNA" datasets.

Usage

SNV

Format

A data frame with 58 columns and 30 rows. The columns indicate the patient sample, and the rows indicate the gene. The contents of the data frame are either NA (indicating no SNV call was made) or one of:

• 1 - nonsynonymous SNV

• 2 - stopgain SNV

• 3 - frameshift insertion

• 4 - frameshift deletion

• 5 - nonframeshift insertion

• 6 - nonframeshift deletion

• 7 - splicing

• 8 - unknown

Author(s)

Christine P'ng

Examples

len <- apply(SNV[1:15], 2, function(x){mutation.count <- length(which(x == 1))});

create.barplot(
    # filename = tempfile(pattern = 'Using_SNV_dataset', fileext = '.tiff'),
    formula = len ~ colnames(SNV[1:15]) ,
    data = SNV,
    main = 'SNV dataset',
    xaxis.rot = 45, 
    ylimits = c(0,30),
    yat = seq(0,30,5),
    description = 'Barplot created by BoutrosLab.plotting.general'
    );

BoutrosLab.plotting.general documentation built on Oct. 4, 2024, 9:07 a.m.