DIPG: applying MultiPLIER

J. Taroni 2018

Apply the MultiPLIER (recount2) model to the two datasets prepped in 34-DIPG_data_cleaning.

Set up

`%>%` <- dplyr::`%>%`
source(file.path("util", "plier_util.R"))

Directories for this notebook

# plot and result directory setup for this notebook
plot.dir <- file.path("plots", "35")
dir.create(plot.dir, recursive = TRUE, showWarnings = FALSE)
results.dir <- file.path("results", "35")
dir.create(results.dir, recursive = TRUE, showWarnings = FALSE)

Read in data

recount2 PLIER model

recount.file <- file.path("data", "recount2_PLIER_data", 
                          "recount_PLIER_model.RDS")
recount.plier <- readRDS(recount.file)

DIPG Expression data

# we want this is matrix form, with the gene symbols as rownames
gse50021 <- readr::read_tsv(file.path("data", "expression_data", 
                                      "GSE50021_mean_agg.pcl")) %>%
  as.data.frame() %>%
  tibble::column_to_rownames("Gene") %>%
  as.matrix()

Parsed with column specification:
cols(
  .default = col_double(),
  Gene = col_character()
)
See spec(...) for full column specifications.

e.geod.file <- 
  file.path("data", "expression_data", 
            "DIPG_E-GEOD-26576_hgu133plus2_SCANfast_with_GeneSymbol.pcl")
gse26576 <- readr::read_tsv(e.geod.file) %>%
  dplyr::select(-EntrezID) %>%
  as.data.frame() %>%
  tibble::column_to_rownames("GeneSymbol") %>%
  as.matrix()

Parsed with column specification:
cols(
  .default = col_double(),
  EntrezID = col_integer(),
  GeneSymbol = col_character()
)
See spec(...) for full column specifications.

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Apply the model

GSE50021

gse50021.b <- GetNewDataB(exprs.mat = gse50021,
                          plier.model = recount.plier)

Loading required package: PLIER
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Loading required package: pheatmap
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-13

Loading required package: knitr
Loading required package: rsvd
Loading required package: qvalue

Save the B matrix to file

saveRDS(gse50021.b, file = file.path(results.dir, "GSE50021_recount2_B.RDS"))

E-GEOD-26576

Now the next expression dataset

gse26576.b <- GetNewDataB(exprs.mat = gse26576,
                          plier.model = recount.plier)

Save to file

saveRDS(gse26576.b, file = file.path(results.dir, 
                                     "E-GEOD-26576_recount2_B.RDS"))