Runs PAM50 and SCMGENE subtype methods on log2 expression data.
A tab delimited file with samplenames as column IDs, gene symbols as row IDs and log2 expression data. Any gene symbol can be present in the file as long as ESR1 and ERBB2 are there, otherwise PAM50 won't work. The more gene symbols matching the PAM50 set the better.
Hugo_symbol EFM192A EVSAT MDAMB453 MDAMB231 MDAMB468 BT549 CAL851 EFM19
A1BG 8.315511 5.454009 7.822566 6.140037 5.111359 7.599171 5.173046 6.038426
A2M 4.107914 3.714508 3.907026 4.059009 7.406219 3.973131 4.741874 3.801728
NAT1 8.914029 8.343696 9.054734 8.80809 8.708712 7.315499 8.805189 6.833612
NAT2 6.564016 4.953733 4.763946 4.644254 4.364252 4.228607 5.419792 4.522074
SERPINA3 8.339674 5.361677 4.422622 4.641157 9.53551 5.258785 11.69059 8.127704
AADAC 4.326528 4.037927 3.680285 3.766857 3.94583 3.694712 4.694278 3.882659
AAMP 9.266102 10.43423 9.745142 8.790493 9.474694 8.564627 8.914895 9.234852
AANAT 4.118585 4.168364 3.84862 3.839901 4.013059 4.515908 3.721725 3.903788
AARS 10.73831 10.82067 10.40384 9.457173 10.26427 10.38802 10.48933 9.772005
Optionally uses prefix before first underscore to group samples togeter. For example, many single cells with the same prefix will be grouped.
MCF-7_01 MCF-7
MCF-7_02 MCF-7
BT474_01 BT474
BT474_02 BT474
Install some libraries
install.packages("ggplot2")
install.packages("gplots")
install.packages("heatmap.plus")
install.packages("reshape")
install.packages("RColorBrewer")
install.packages("devtools")
source("http://bioconductor.org/biocLite.R")
biocLite("genefu")
biocLite("ctc")
biocLite("org.Hs.eg.db")
biocLite("impute")
Load them up
library(ggplot2)
library(gplots)
library(org.Hs.eg.db)
library(heatmap.plus)
library(reshape)
library(RColorBrewer)
library(genefu)
library(ctc)
library(devtools)
library(impute)
Install and load BASALT
install_github("elswob/BASALT")
library(BASALT)
Need three arguements:
- The name of the directory for the output
- The full path and name of the expression data file
- A short name for the data
Example breast cancer data from the Cancer Cell Line Encyclopedia (CCLE) is available for testing.
s=system.file("extdata","CCLE.tsv",package="BASALT")
run_basalt("~/subtype_test",s,"ccle")
- A combined tsv file for all subtype methods (subtype_summary.tsv)
- Detailed output from PAM50 and SCMGENE, including:
| File | Description |
|---|---|
| BASALT.conf | A configuration file with details of the analysis run |
| subtype_summary.tsv | A summary of all subtype calls for all samples |
| subtype_summary_pc.pdf | A summary plot of all subtype calls by percentage |
| subtype_summary_counts.pdf | A summary plot of all subtype calls by counts |
| scmgene/pam50_robus_classification_plot_grouped.pdf | A plot of subtype calls for the genefu robust PAM50 method by percentage |
| PAM50/classification_plot_grouped_counts.pdf | A plot of PAM50 subtype calls by counts |
| PAM50/classification_plot_grouped_pc.pdf | A plot of PAM50 subtype calls by percentage |
| PAM50/heatmap_median_centered.pdf | A heatmap displaying unsupervised hierarchincal clustering of the median centred data |
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] impute_1.42.0 ctc_1.42.0 amap_0.8-14 RColorBrewer_1.1-2 reshape_0.8.5 heatmap.plus_1.3 genefu_1.18.0 biomaRt_2.24.0
[9] mclust_5.0.1 survcomp_1.18.0 prodlim_1.5.1 survival_2.38-3 org.Hs.eg.db_3.1.2 RSQLite_1.0.0 DBI_0.3.1 AnnotationDbi_1.30.1
[17] GenomeInfoDb_1.4.1 IRanges_2.2.5 S4Vectors_0.6.1 Biobase_2.28.0 BiocGenerics_0.14.0 gplots_2.17.0 ggplot2_1.0.1 BASALT_0.1
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 plyr_1.8.3 bitops_1.0-6 tools_3.2.0 digest_0.6.8 gtable_0.1.2 proto_0.3-10 bootstrap_2015.2 stringr_1.0.0
[10] SuppDists_1.1-9.1 gtools_3.5.0 caTools_1.17.1 XML_3.98-1.3 gdata_2.17.0 lava_1.4.1 rmeta_2.16 reshape2_1.4.1 magrittr_1.5
[19] scales_0.2.5 survivalROC_1.0.3 MASS_7.3-42 splines_3.2.0 colorspace_1.2-6 labeling_0.3 KernSmooth_2.23-15 stringi_0.5-5 RCurl_1.95-4.7
[28] munsell_0.4.2