patient {BoutrosLab.plotting.general}R Documentation

Dataset describing qualities of 58 colon cancer patients

Description

A number of qualities describing 58 colon cancer patients. The same patient samples are described in the "microarray", "SNV" and "CNA" datasets.

Usage

patient

Format

A data frame with 5 columns and 58 rows. Each row indicates a different patient sample, with the following columns describing a feature of the sample:

sex

The sex of the paient, either "male" or "female"

stage

The stage of the patient's cancer, one of "I", "II", "III", "IV", or NA

msi

The microsatellite instabiltiy of the cancer, either "MSS" or "MSI-High"

prop.CAGT

The proportion of C to A or G to T base changes between the sample and reference genome

prop.CTGA

The proportion of C to T or G to A base changes between the sample and reference genome

prop.CGGC

The proportion of C to G or G to C base changes between the sample and reference genome

prop.TAAT

The proportion of T to A or A to T base changes between the sample and reference genome

prop.TGAC

The proportion of T to G or A to C base changes between the sample and reference genome

prop.TCAG

The proportion of T to C or A to G base changes between the sample and reference genome

Author(s)

Christine P'ng

Examples

# use sample to set colour scheme
sex.colours <- replace(as.vector(patient$sex), which(patient$sex == 'male'),'dodgerblue');
sex.colours <- replace(sex.colours, which(patient$sex == 'female'), 'pink');
len <- apply(SNV[1:15], 2, function(x){mutation.count <- length(which(x == 1))});

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

[Package BoutrosLab.plotting.general version 6.0.3 Index]