Code chunk: "setup"

Preamble

The purpose of this document is to show how R Markdown can be used to generate a report in HTML format.

The data

We’ll be using an extended version of the METABRIC data set in which columns have been added for the mRNA expression values for selected genes, including estrogen receptor alpha (ESR1), progesterone receptor (PGR), GATA3 and FOXA1.

The METABRIC study characterized the genomic mutations and gene expression profiles for over 2000 primary breast tumours.

Curtis et al., Nature 486:346-52, 2012

Pereira et al., Nature Communications 7:11479, 2016

Both the clinical data and the gene expression values were downloaded from cBioPortal.

metabric <- read_csv("data/metabric_clinical_and_expression_data.csv") %>%
    select(Patient_ID,
           ER_status,
           HER2_status,
           `3-gene_classifier`,
           PAM50, ESR1, ERBB2, PGR, TP53, PIK3CA, GATA3, FOXA1, MLPH)

The table below shows the first few rows of the data for the first 7 columns.

Code chunk: top few rows of table. Note the alignment in the columns.
Patient_ID ER_status HER2_status 3-gene_classifier PAM50 ESR1 ERBB2
MB-0000 Positive Negative ER-/HER2- claudin-low 8.93 9.33
MB-0002 Positive Negative ER+/HER2- High Prolif LumA 10.05 9.73
MB-0005 Positive Negative NA LumB 10.04 9.73
MB-0006 Positive Negative NA LumB 10.40 10.33
MB-0008 Positive Negative ER+/HER2- High Prolif LumB 11.28 9.96
MB-0010 Positive Negative ER+/HER2- High Prolif LumB 11.24 9.74
MB-0014 Positive Negative NA LumB 10.79 9.28
MB-0022 Positive Negative NA claudin-low 10.44 8.61

Gene expression by ER status

The figures below show gene expression distribution separated according to ER status. The data are further split by HER2 status.

Four genes are shown:

  • ESR1
  • ERBB2
  • GATA3
  • TP53
Code chunks: 1 chunk - set colours for plotting. 4 chunks - one for each plot.

ESR1

ERBB2

GATA3

TP53

PAM50 cancer subtype

The PAM50 classification of breast cancer included 5 basic subtypes. An additional “claudin low” subtype is also included in metabric and some tumours are not classified (NC). The seven categories included in metabric are:

Category Description
Basal Basal-like
Her2 HER2 enriched
LumA Luminal A
LumB Luminal B
NC Not classified
Normal Normal-like
claudin-low Claudin Low

The table below shows the mean gene expression for 8 genes across all samples according to their PAM50 cancer subtype.

Code chunk: summarise expression data and generate table
PAM50 ESR1 ERBB2 PGR TP53 PIK3CA GATA3 FOXA1 MLPH
claudin-low 6.68 9.69 5.45 6.23 5.95 7.40 9.47 9.48
LumA 10.93 10.65 6.67 6.20 5.90 10.43 11.65 12.25
LumB 11.16 10.45 6.14 6.18 5.97 10.29 11.61 11.98
Her2 7.02 13.07 5.40 6.03 5.96 8.78 11.14 11.55
Normal 9.76 10.54 5.97 6.14 5.85 9.67 11.12 11.90
Basal 6.00 9.91 5.36 6.24 6.08 7.15 6.72 8.21
NC 10.83 10.23 6.25 6.22 5.66 10.29 11.18 11.92

Three gene classifier

Here we look at GATA3 and ESR1 expression according to the three gene classifier.

Code chunk: 4 plots arranged using `patchwork`. Caption in chunk options.
Expression of ESR1 and GATA3 according to 3-gene classifier. (a) Bar plot showing numbers of samples in each category. (b) Scatter plot showing ESR1 expression against GAT3 expression for each sample. (c) Violin plot showing distribution of ESR1 expression. (d) Violin plot showing distribution of GATA3 expression.

Expression of ESR1 and GATA3 according to 3-gene classifier. (a) Bar plot showing numbers of samples in each category. (b) Scatter plot showing ESR1 expression against GAT3 expression for each sample. (c) Violin plot showing distribution of ESR1 expression. (d) Violin plot showing distribution of GATA3 expression.

END OF REPORT

Session Info

devtools::session_info()
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