cmapR Tutorial
Introduction
This notebook will walk through some of the basic functionality in the cmapR package, which is largely centered around working with matrix data in GCT and GCTX format, commonly used by the Connectivity Map (CMap) project.
Installation
The cmapR package can be installed from Bioconductor by running the following commands in an R session.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cmapR")## Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)## Warning: package(s) not installed when version(s) same as or greater than current; use
## `force = TRUE` to re-install: 'cmapR'## Old packages: 'curl', 'fontawesome', 'boot', 'foreign', 'lattice', 'nlme'cmapR source code can be also obtained from github.
Loading the cmapR package
cmapR can be loaded within an R session or script just like any other package.
## Warning: multiple methods tables found for 'union'## Warning: multiple methods tables found for 'intersect'## Warning: multiple methods tables found for 'setdiff'GCT objects in R
The main class of objects in cmapR is the
GCT class. The GCT object contains a data
matrix and (optionally) row and column annotations as
data.frame objects. cmapR has comes with an example GCT
object called ds (short for dataset). We can view its
structure by simply typing its name.
## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:978, 1:272] -0.524 -0.372 0.578 0.569 1.48 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:978] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. .. ..$ : chr [1:272] "CPC006_A549_6H:BRD-U88459701-000-01-8:10" "CPC020_A375_6H:BRD-A82307304-001-01-8:10" "CPC020_HT29_6H:BRD-A82307304-001-01-8:10" "CPC020_PC3_24H:BRD-A82307304-001-01-8:10" ...
## ..@ rid : chr [1:978] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ cid : chr [1:272] "CPC006_A549_6H:BRD-U88459701-000-01-8:10" "CPC020_A375_6H:BRD-A82307304-001-01-8:10" "CPC020_HT29_6H:BRD-A82307304-001-01-8:10" "CPC020_PC3_24H:BRD-A82307304-001-01-8:10" ...
## ..@ rdesc :'data.frame': 978 obs. of 6 variables:
## .. ..$ id : chr [1:978] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. ..$ is_bing : int [1:978] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ is_lm : int [1:978] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ pr_gene_id : int [1:978] 5720 466 6009 2309 387 3553 427 5898 23365 6657 ...
## .. ..$ pr_gene_symbol: chr [1:978] "PSME1" "ATF1" "RHEB" "FOXO3" ...
## .. ..$ pr_gene_title : chr [1:978] "proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)" "activating transcription factor 1" "Ras homolog enriched in brain" "forkhead box O3" ...
## ..@ cdesc :'data.frame': 272 obs. of 16 variables:
## .. ..$ brew_prefix : chr [1:272] "CPC006_A549_6H" "CPC020_A375_6H" "CPC020_HT29_6H" "CPC020_PC3_24H" ...
## .. ..$ cell_id : chr [1:272] "A549" "A375" "HT29" "PC3" ...
## .. ..$ distil_cc_q75 : num [1:272] 0.18 0.46 0.14 0.57 0.2 ...
## .. ..$ distil_nsample : int [1:272] 4 5 4 5 7 5 3 2 2 2 ...
## .. ..$ distil_ss : num [1:272] 2.65 3.21 2.14 4.62 2.27 ...
## .. ..$ id : chr [1:272] "CPC006_A549_6H:BRD-U88459701-000-01-8:10" "CPC020_A375_6H:BRD-A82307304-001-01-8:10" "CPC020_HT29_6H:BRD-A82307304-001-01-8:10" "CPC020_PC3_24H:BRD-A82307304-001-01-8:10" ...
## .. ..$ is_gold : int [1:272] 0 1 0 1 1 1 1 0 0 1 ...
## .. ..$ ngenes_modulated_dn_lm: int [1:272] 15 14 4 67 8 95 42 20 14 80 ...
## .. ..$ ngenes_modulated_up_lm: int [1:272] 10 17 7 50 6 98 19 21 14 36 ...
## .. ..$ pct_self_rank_q25 : num [1:272] 5.526 1.567 9.072 0 0.353 ...
## .. ..$ pert_id : chr [1:272] "BRD-U88459701" "BRD-A82307304" "BRD-A82307304" "BRD-A82307304" ...
## .. ..$ pert_idose : chr [1:272] "10 <b5>M" "10 <b5>M" "10 <b5>M" "10 <b5>M" ...
## .. ..$ pert_iname : chr [1:272] "atorvastatin" "atorvastatin" "atorvastatin" "atorvastatin" ...
## .. ..$ pert_itime : chr [1:272] "6 h" "6 h" "6 h" "24 h" ...
## .. ..$ pert_type : chr [1:272] "trt_cp" "trt_cp" "trt_cp" "trt_cp" ...
## .. ..$ pool_id : chr [1:272] "epsilon" "epsilon" "epsilon" "epsilon" ...
## ..@ version: chr(0)
## ..@ src : chr "inst/extdata/modzs_n272x978.gctx"GCT objects contain the following components, or
slots.
mat- the data matrixrdesc- adata.frameof row annotations, with one row per matrix rowcdesc- adata.frameof column annotations, with one row per matrix columnrid- a character vector of unique row identifierscid- a character vector of unique column identifierssrc- a character string indicating the source (usually a file path) of the data
Accessing GCT object components
The components of a GCT object can be accessed or
modified using a set of accessor functions.
# access the data matrix
m <- mat(ds)
# access the row and column metadata
rdesc <- meta(ds, dimension = "row")
cdesc <- meta(ds, dimension = "column")
# access the row and column ids
rid <- ids(ds, dimension = "row")
cid <- ids(ds, dimension = "column")# update the matrix data to set some values to zero
# note that the updated matrix must be the of the same dimensions as
# the current matrix
m[1:10, 1:10] <- 0
mat(ds) <- m
# replace row and column metadata
meta(ds, dimension = "row") <- data.frame(x=sample(letters, nrow(m),
replace=TRUE))
meta(ds, dimension = "column") <- data.frame(x=sample(letters, ncol(m),
replace=TRUE))
# replace row and column ids
ids(ds, dimension = "row") <- as.character(seq_len(nrow(m)))
ids(ds, dimension = "column") <- as.character(seq_len(ncol(m)))
# and let's look at the modified object
ds## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:978, 1:272] 0 0 0 0 0 0 0 0 0 0 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:978] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. .. ..$ : chr [1:272] "CPC006_A549_6H:BRD-U88459701-000-01-8:10" "CPC020_A375_6H:BRD-A82307304-001-01-8:10" "CPC020_HT29_6H:BRD-A82307304-001-01-8:10" "CPC020_PC3_24H:BRD-A82307304-001-01-8:10" ...
## ..@ rid : chr [1:978] "1" "2" "3" "4" ...
## ..@ cid : chr [1:272] "1" "2" "3" "4" ...
## ..@ rdesc :'data.frame': 978 obs. of 1 variable:
## .. ..$ x: chr [1:978] "m" "p" "f" "w" ...
## ..@ cdesc :'data.frame': 272 obs. of 1 variable:
## .. ..$ x: chr [1:272] "c" "l" "r" "z" ...
## ..@ version: chr(0)
## ..@ src : chr "inst/extdata/modzs_n272x978.gctx"Parsing GCTX files
You can parse both GCT and GCTX files using the
parse_gctx method. This method will read the corresponding
GCT or GCTX file and return an object of class GCT into
your R session.
Parsing the entire file
If the file is small enough to fit in memory, you can parse the entire file at once.
# create a variable to store the path to the GCTX file
# here we'll use a file that's internal to the cmapR package, but
# in practice this could be any valid path to a GCT or GCTX file
ds_path <- system.file("extdata", "modzs_n25x50.gctx", package="cmapR")
my_ds <- parse_gctx(ds_path)## reading /tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx## doneYou can view the structure of this newly-created GCT object just by typing its name.
## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:50, 1:25] -1.145 -1.165 0.437 0.139 -0.673 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. .. ..$ : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rid : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ cid : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rdesc :'data.frame': 50 obs. of 6 variables:
## .. ..$ id : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. ..$ is_bing : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ is_lm : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ pr_gene_id : int [1:50] 5720 466 6009 2309 387 3553 427 5898 23365 6657 ...
## .. ..$ pr_gene_symbol: chr [1:50] "PSME1" "ATF1" "RHEB" "FOXO3" ...
## .. ..$ pr_gene_title : chr [1:50] "proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)" "activating transcription factor 1" "Ras homolog enriched in brain" "forkhead box O3" ...
## ..@ cdesc :'data.frame': 25 obs. of 16 variables:
## .. ..$ brew_prefix : chr [1:25] "CPC004_PC3_24H" "BRAF001_HEK293T_24H" "CPC006_HT29_24H" "CVD001_HEPG2_24H" ...
## .. ..$ cell_id : chr [1:25] "PC3" "HEK293T" "HT29" "HEPG2" ...
## .. ..$ distil_cc_q75 : num [1:25] 0.05 0.1 0.17 0.45 0.24 ...
## .. ..$ distil_nsample : int [1:25] 5 9 4 3 4 5 2 3 2 2 ...
## .. ..$ distil_ss : num [1:25] 2.9 1.88 2.71 4.06 3.83 ...
## .. ..$ id : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## .. ..$ is_gold : int [1:25] 0 0 0 1 1 0 1 0 0 0 ...
## .. ..$ ngenes_modulated_dn_lm: int [1:25] 11 3 8 38 36 23 12 11 33 13 ...
## .. ..$ ngenes_modulated_up_lm: int [1:25] 10 7 25 40 16 17 23 14 37 22 ...
## .. ..$ pct_self_rank_q25 : num [1:25] 26.904 17.125 7.06 0.229 4.686 ...
## .. ..$ pert_id : chr [1:25] "BRD-A51714012" "BRD-U73308409" "BRD-U88459701" "BRD-U88459701" ...
## .. ..$ pert_idose : chr [1:25] "10 <b5>M" "500 nM" "10 <b5>M" "10 <b5>M" ...
## .. ..$ pert_iname : chr [1:25] "venlafaxine" "vemurafenib" "atorvastatin" "atorvastatin" ...
## .. ..$ pert_itime : chr [1:25] "24 h" "24 h" "24 h" "24 h" ...
## .. ..$ pert_type : chr [1:25] "trt_cp" "trt_cp" "trt_cp" "trt_cp" ...
## .. ..$ pool_id : chr [1:25] "epsilon" "epsilon" "epsilon" "epsilon" ...
## ..@ version: chr(0)
## ..@ src : chr "/tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx"As you can see from looking at the @mat slot, this small
dataset has 50 rows and 25 columns.
Parsing a susbset of the file
Note: only GCTX files (not GCT) support parsing subsets.
When working with large GCTX files, it is usually not possible to read the entire file into memory all at once. In these cases, it’s helpful to read subsets of the data. These subsets can be defined by numeric row or column index, as shown below.
# read just the first 10 columns, using numeric indices
(my_ds_10_columns <- parse_gctx(ds_path, cid=1:10))## reading /tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx## done## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:50, 1:10] -1.145 -1.165 0.437 0.139 -0.673 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. .. ..$ : chr [1:10] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rid : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ cid : chr [1:10] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rdesc :'data.frame': 50 obs. of 6 variables:
## .. ..$ id : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. ..$ is_bing : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ is_lm : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ pr_gene_id : int [1:50] 5720 466 6009 2309 387 3553 427 5898 23365 6657 ...
## .. ..$ pr_gene_symbol: chr [1:50] "PSME1" "ATF1" "RHEB" "FOXO3" ...
## .. ..$ pr_gene_title : chr [1:50] "proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)" "activating transcription factor 1" "Ras homolog enriched in brain" "forkhead box O3" ...
## ..@ cdesc :'data.frame': 10 obs. of 16 variables:
## .. ..$ brew_prefix : chr [1:10] "CPC004_PC3_24H" "BRAF001_HEK293T_24H" "CPC006_HT29_24H" "CVD001_HEPG2_24H" ...
## .. ..$ cell_id : chr [1:10] "PC3" "HEK293T" "HT29" "HEPG2" ...
## .. ..$ distil_cc_q75 : num [1:10] 0.05 0.1 0.17 0.45 0.24 ...
## .. ..$ distil_nsample : int [1:10] 5 9 4 3 4 5 2 3 2 2
## .. ..$ distil_ss : num [1:10] 2.9 1.88 2.71 4.06 3.83 ...
## .. ..$ id : chr [1:10] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## .. ..$ is_gold : int [1:10] 0 0 0 1 1 0 1 0 0 0
## .. ..$ ngenes_modulated_dn_lm: int [1:10] 11 3 8 38 36 23 12 11 33 13
## .. ..$ ngenes_modulated_up_lm: int [1:10] 10 7 25 40 16 17 23 14 37 22
## .. ..$ pct_self_rank_q25 : num [1:10] 26.904 17.125 7.06 0.229 4.686 ...
## .. ..$ pert_id : chr [1:10] "BRD-A51714012" "BRD-U73308409" "BRD-U88459701" "BRD-U88459701" ...
## .. ..$ pert_idose : chr [1:10] "10 <b5>M" "500 nM" "10 <b5>M" "10 <b5>M" ...
## .. ..$ pert_iname : chr [1:10] "venlafaxine" "vemurafenib" "atorvastatin" "atorvastatin" ...
## .. ..$ pert_itime : chr [1:10] "24 h" "24 h" "24 h" "24 h" ...
## .. ..$ pert_type : chr [1:10] "trt_cp" "trt_cp" "trt_cp" "trt_cp" ...
## .. ..$ pool_id : chr [1:10] "epsilon" "epsilon" "epsilon" "epsilon" ...
## ..@ version: chr(0)
## ..@ src : chr "/tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx"As expected, we see that we’ve now got a 10-column dataset.
More commonly, we’ll want to identify a subset of the data that is of
particular interest and read only those rows and/or columns. In either
case, we’ll use the rid and/or cid arguments
to parse_gctx to extract only the data we want. In this
example, we’ll use the GCTX file’s embedded column annotations to
identify the columns corresponding to the compound vemurafenib
and then read only those columns. We can extract these annotations using
the read_gctx_meta function.
# read the column metadata
col_meta <- read_gctx_meta(ds_path, dim="col")
# figure out which signatures correspond to vorinostat by searching the 'pert_iname' column
idx <- which(col_meta$pert_iname=="vemurafenib")
# read only those columns from the GCTX file by using the 'cid' parameter
vemurafenib_ds <- parse_gctx(ds_path, cid=idx)## reading /tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx## doneIn the example above we used numeric column indices, but the
rid and cid arguments also accept character
vectors of ids. The following is equally valid.
# get a vector of character ids, using the id column in col_meta
col_ids <- col_meta$id[idx]
vemurafenib_ds2 <- parse_gctx(ds_path, cid=col_ids)## reading /tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx## done## [1] TRUECreating a GCT object from existing workspace objects
It’s also possible to create a GCT object from existing
objects in your R workspace. You will minimally need to have a matrix
object, but can also optionally include data.frames of row
and column annotations. This is done using the new
constructor function.
# initialize a matrix object
# note that you either must assign values to the rownames and colnames
# of the matrix, or pass them,
# as the 'rid' and 'cid' arguments to GCT"
m <- matrix(stats::rnorm(100), ncol=10)
rownames(m) <- letters[1:10]
colnames(m) <- LETTERS[1:10]
(my_new_ds <- new("GCT", mat=m))## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:10, 1:10] -1.783 0.439 -0.768 0.598 2.376 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:10] "a" "b" "c" "d" ...
## .. .. ..$ : chr [1:10] "A" "B" "C" "D" ...
## ..@ rid : chr [1:10] "a" "b" "c" "d" ...
## ..@ cid : chr [1:10] "A" "B" "C" "D" ...
## ..@ rdesc :'data.frame': 0 obs. of 0 variables
## Formal class 'data.frame' [package "methods"] with 4 slots
## .. .. ..@ .Data : list()
## .. .. ..@ names : chr(0)
## .. .. ..@ row.names: int(0)
## .. .. ..@ .S3Class : chr "data.frame"
## ..@ cdesc :'data.frame': 0 obs. of 0 variables
## Formal class 'data.frame' [package "methods"] with 4 slots
## .. .. ..@ .Data : list()
## .. .. ..@ names : chr(0)
## .. .. ..@ row.names: int(0)
## .. .. ..@ .S3Class : chr "data.frame"
## ..@ version: chr(0)
## ..@ src : chr(0)# we can also include the row/column annotations as data.frames
# note these are just arbitrary annotations used to illustrate the function call
rdesc <- data.frame(id=letters[1:10], type=rep(c(1, 2), each=5))
cdesc <- data.frame(id=LETTERS[1:10], type=rep(c(3, 4), each=5))
(my_new_ds <- new("GCT", mat=m, rdesc=rdesc, cdesc=cdesc))## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:10, 1:10] -1.783 0.439 -0.768 0.598 2.376 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:10] "a" "b" "c" "d" ...
## .. .. ..$ : chr [1:10] "A" "B" "C" "D" ...
## ..@ rid : chr [1:10] "a" "b" "c" "d" ...
## ..@ cid : chr [1:10] "A" "B" "C" "D" ...
## ..@ rdesc :'data.frame': 10 obs. of 2 variables:
## .. ..$ id : chr [1:10] "a" "b" "c" "d" ...
## .. ..$ type: num [1:10] 1 1 1 1 1 2 2 2 2 2
## ..@ cdesc :'data.frame': 10 obs. of 2 variables:
## .. ..$ id : chr [1:10] "A" "B" "C" "D" ...
## .. ..$ type: num [1:10] 3 3 3 3 3 4 4 4 4 4
## ..@ version: chr(0)
## ..@ src : chr(0)Adding annotations to a GCT object
When working with GCT objects, it’s often convenient to
have the row and column annotations embedded as the rdesc
and cdesc slots, respectively. If these metadata are stored
separatly from the GCTX file itself, you can read them in separately and
then apply them to the GCT object using the
annotate.gct function. Let’s parse the dataset again, only
this time reading only the matrix. We’ll then apply the column
annotations we read in previously.
# we'll use the matrix_only argument to extract just the matrix
(my_ds_no_meta <- parse_gctx(ds_path, matrix_only = TRUE))## reading /tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx## done## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:50, 1:25] -1.145 -1.165 0.437 0.139 -0.673 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. .. ..$ : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rid : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ cid : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rdesc :'data.frame': 50 obs. of 1 variable:
## .. ..$ id: chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ cdesc :'data.frame': 25 obs. of 1 variable:
## .. ..$ id: chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ version: chr(0)
## ..@ src : chr "/tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx"Note in this case that cmapR still populates 1-column
data.frames containing the row and column ids, but the rest
of the annotations have been omitted.
Now we’ll apply the column annotations using
annotate.gct.
# note we need to specifiy which dimension to annotate (dim)
# and which column in the annotations corresponds to the column
# ids in the matrix (keyfield)
(my_ds_no_meta <- annotate_gct(my_ds_no_meta, col_meta, dim="col",
keyfield="id"))## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:50, 1:25] -1.145 -1.165 0.437 0.139 -0.673 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. .. ..$ : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rid : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ cid : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ rdesc :'data.frame': 50 obs. of 1 variable:
## .. ..$ id: chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ cdesc :'data.frame': 25 obs. of 16 variables:
## .. ..$ id : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## .. ..$ brew_prefix : chr [1:25] "CPC004_PC3_24H" "BRAF001_HEK293T_24H" "CPC006_HT29_24H" "CVD001_HEPG2_24H" ...
## .. ..$ cell_id : chr [1:25] "PC3" "HEK293T" "HT29" "HEPG2" ...
## .. ..$ distil_cc_q75 : num [1:25] 0.05 0.1 0.17 0.45 0.24 ...
## .. ..$ distil_nsample : int [1:25] 5 9 4 3 4 5 2 3 2 2 ...
## .. ..$ distil_ss : num [1:25] 2.9 1.88 2.71 4.06 3.83 ...
## .. ..$ is_gold : int [1:25] 0 0 0 1 1 0 1 0 0 0 ...
## .. ..$ ngenes_modulated_dn_lm: int [1:25] 11 3 8 38 36 23 12 11 33 13 ...
## .. ..$ ngenes_modulated_up_lm: int [1:25] 10 7 25 40 16 17 23 14 37 22 ...
## .. ..$ pct_self_rank_q25 : num [1:25] 26.904 17.125 7.06 0.229 4.686 ...
## .. ..$ pert_id : chr [1:25] "BRD-A51714012" "BRD-U73308409" "BRD-U88459701" "BRD-U88459701" ...
## .. ..$ pert_idose : chr [1:25] "10 <b5>M" "500 nM" "10 <b5>M" "10 <b5>M" ...
## .. ..$ pert_iname : chr [1:25] "venlafaxine" "vemurafenib" "atorvastatin" "atorvastatin" ...
## .. ..$ pert_itime : chr [1:25] "24 h" "24 h" "24 h" "24 h" ...
## .. ..$ pert_type : chr [1:25] "trt_cp" "trt_cp" "trt_cp" "trt_cp" ...
## .. ..$ pool_id : chr [1:25] "epsilon" "epsilon" "epsilon" "epsilon" ...
## ..@ version: chr(0)
## ..@ src : chr "/tmp/RtmpaOGCOU/Rinst1104644bd752/cmapR/extdata/modzs_n25x50.gctx"Note how now the cdesc slot is populated after
annotating.
Slicing a GCT object
Just as it’s possible to read a subset of rows or columns from a GCTX
file, it is also possible to extract a subset of rows or columns from a
GCT object in memory. This is done with the
subset_gct function. Just like parse_gctx,
this function uses rid and cid parameters to
determine which rows and columns to extract. Let’s extract the
vemurafenib columns from the my_ds object in
memory.
# in memory slice using the cid parameter
vemurafenib_ds3 <- subset_gct(my_ds,
cid=which(col_meta$pert_iname=="vemurafenib"))
identical(vemurafenib_ds, vemurafenib_ds3)## [1] FALSEMelting GCT objects
It’s often useful to have data stored in long form
data.frame objects, especially for compatibility with
plotting libraries like ggplot2. It’s
possible to convert a GCT object into this long form by
using the melt_gct function, which relies on the
melt function in the data.table
package.
## melting GCT object...## done# plot the matrix values grouped by gene
grps <- with(vemurafenib_ds3_melted, split(value, pr_gene_symbol))
boxplot(grps)
Merging two GCT objects
You can combine two independent GCT objects using the
merge_gct function. Note that it is important to specify
which dimension (row or column) you wish to merge on and that the two
GCT objects in question share one common dimension.
Math operations on GCT objects
The @mat slot of a GCT object is a base R matrix object,
so it’s possible to perform standard math operations on this matrix.
This matrix can be accessed directly, i.e. my_ds@mat, but
can also be extracted using the get_gct_matrix function
from cmapR. Below are a few simple examples, but these can
easily be extended, particulary through use of the apply
function.
Now let’s perform a few simple math operations
# compute the row and column means
row_means <- rowMeans(m)
col_means <- colMeans(m)
message("means:")## means:## 200814_at 222103_at 201453_x_at 204131_s_at 200059_s_at 205067_at
## -0.04539519 -0.36639891 -0.40457100 0.35614147 0.40454578 -0.22763633## CPC004_PC3_24H:BRD-A51714012-001-03-1:10
## 0.04775844
## BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625
## -0.01296067
## CPC006_HT29_24H:BRD-U88459701-000-01-8:10
## -0.20454084
## CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10
## -0.26358546
## NMH001_NEU_6H:BRD-K69726342-001-02-6:10
## -0.44564062
## CPC020_VCAP_6H:BRD-A82307304-001-01-8:10
## -0.08844710# using 'apply', compute the max of each row and column
row_max <- apply(m, 1, max)
col_max <- apply(m, 2, max)
message("maxes:")## maxes:## 200814_at 222103_at 201453_x_at 204131_s_at 200059_s_at 205067_at
## 1.204220 1.829283 1.022154 2.507013 3.064311 1.876900## CPC004_PC3_24H:BRD-A51714012-001-03-1:10
## 1.8241825
## BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625
## 0.8706381
## CPC006_HT29_24H:BRD-U88459701-000-01-8:10
## 2.5714328
## CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10
## 3.0643106
## NMH001_NEU_6H:BRD-K69726342-001-02-6:10
## 1.8993782
## CPC020_VCAP_6H:BRD-A82307304-001-01-8:10
## 0.8148650GCT-specific math functions
cmapR also contains a handful of math functions designed
specifically for operating on GCT objects.
# transposing a GCT object - also swaps row and column annotations
(my_ds_transpose <- transpose_gct(my_ds))## Formal class 'GCT' [package "cmapR"] with 7 slots
## ..@ mat : num [1:25, 1:50] -1.145 0.142 -0.469 0.457 0.483 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## .. .. ..$ : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ rid : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## ..@ cid : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## ..@ rdesc :'data.frame': 25 obs. of 16 variables:
## .. ..$ brew_prefix : chr [1:25] "CPC004_PC3_24H" "BRAF001_HEK293T_24H" "CPC006_HT29_24H" "CVD001_HEPG2_24H" ...
## .. ..$ cell_id : chr [1:25] "PC3" "HEK293T" "HT29" "HEPG2" ...
## .. ..$ distil_cc_q75 : num [1:25] 0.05 0.1 0.17 0.45 0.24 ...
## .. ..$ distil_nsample : int [1:25] 5 9 4 3 4 5 2 3 2 2 ...
## .. ..$ distil_ss : num [1:25] 2.9 1.88 2.71 4.06 3.83 ...
## .. ..$ id : chr [1:25] "CPC004_PC3_24H:BRD-A51714012-001-03-1:10" "BRAF001_HEK293T_24H:BRD-U73308409-000-01-9:0.625" "CPC006_HT29_24H:BRD-U88459701-000-01-8:10" "CVD001_HEPG2_24H:BRD-U88459701-000-01-8:10" ...
## .. ..$ is_gold : int [1:25] 0 0 0 1 1 0 1 0 0 0 ...
## .. ..$ ngenes_modulated_dn_lm: int [1:25] 11 3 8 38 36 23 12 11 33 13 ...
## .. ..$ ngenes_modulated_up_lm: int [1:25] 10 7 25 40 16 17 23 14 37 22 ...
## .. ..$ pct_self_rank_q25 : num [1:25] 26.904 17.125 7.06 0.229 4.686 ...
## .. ..$ pert_id : chr [1:25] "BRD-A51714012" "BRD-U73308409" "BRD-U88459701" "BRD-U88459701" ...
## .. ..$ pert_idose : chr [1:25] "10 <b5>M" "500 nM" "10 <b5>M" "10 <b5>M" ...
## .. ..$ pert_iname : chr [1:25] "venlafaxine" "vemurafenib" "atorvastatin" "atorvastatin" ...
## .. ..$ pert_itime : chr [1:25] "24 h" "24 h" "24 h" "24 h" ...
## .. ..$ pert_type : chr [1:25] "trt_cp" "trt_cp" "trt_cp" "trt_cp" ...
## .. ..$ pool_id : chr [1:25] "epsilon" "epsilon" "epsilon" "epsilon" ...
## ..@ cdesc :'data.frame': 50 obs. of 6 variables:
## .. ..$ id : chr [1:50] "200814_at" "222103_at" "201453_x_at" "204131_s_at" ...
## .. ..$ is_bing : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ is_lm : int [1:50] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ pr_gene_id : int [1:50] 5720 466 6009 2309 387 3553 427 5898 23365 6657 ...
## .. ..$ pr_gene_symbol: chr [1:50] "PSME1" "ATF1" "RHEB" "FOXO3" ...
## .. ..$ pr_gene_title : chr [1:50] "proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)" "activating transcription factor 1" "Ras homolog enriched in brain" "forkhead box O3" ...
## ..@ version: chr(0)
## ..@ src : chr(0)# converting a GCT object's matrix to ranks
# the 'dim' option controls the direction along which the ranks are calculated
my_ds_rank_by_column <- rank_gct(my_ds, dim="col")
# plot z-score vs rank for the first 25 genes (rows)
ranked_m <- mat(my_ds_rank_by_column)
plot(ranked_m[1:25, ],
m[1:25, ],
xlab="rank",
ylab="differential expression score",
main="score vs. rank")
Writing GCT objects to disk
GCT objects can be written to disk either in GCT or GCTX
format using the write_gct and write_gctx
functions, respectively.
## Saving file to ./my_ds_n25x50.gct
## Dimensions of matrix: [50x25]
## Setting precision to 4
## Saved.## writing ./my_ds_n25x50.gctx## chunk sizes: 50 25# write_gctx can also compress the dataset upon write,
# which can be controlled using the 'compression_level' option.
# the higher the value, the greater the compression, but the
# longer the read/write time
write_gctx(my_ds, "my_ds_compressed", compression_level = 9)## writing ./my_ds_compressed_n25x50.gctx
## chunk sizes: 50 25Converting GCT objects to SummarizedExperiment objects
The GCT class is quite similar in spirit to the
SummarizedExperiment class from the
SummarizedExperiment package (citation). Converting a
GCT object to a SummarizedExeriment object is
straightforward, as shown below.
## class: SummarizedExperiment
## dim: 978 272
## metadata(0):
## assays(1): exprs
## rownames(978): 200814_at 222103_at ... 203341_at 205379_at
## rowData names(1): x
## colnames(272): CPC006_A549_6H:BRD-U88459701-000-01-8:10
## CPC020_A375_6H:BRD-A82307304-001-01-8:10 ...
## CPD002_PC3_6H:BRD-A51714012-001-04-9:10
## CPD002_PC3_24H:BRD-A51714012-001-04-9:10
## colData names(1): xSession Info
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] cmapR_1.19.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 generics_0.1.3
## [3] SparseArray_1.7.2 lattice_0.22-6
## [5] digest_0.6.37 evaluate_1.0.1
## [7] grid_4.4.2 fastmap_1.2.0
## [9] jsonlite_1.8.9 Matrix_1.7-1
## [11] GenomeInfoDb_1.43.1 BiocManager_1.30.25
## [13] httr_1.4.7 UCSC.utils_1.3.0
## [15] jquerylib_0.1.4 abind_1.4-8
## [17] cli_3.6.3 rlang_1.1.4
## [19] RProtoBufLib_2.19.0 crayon_1.5.3
## [21] XVector_0.47.0 Biobase_2.67.0
## [23] cachem_1.1.0 DelayedArray_0.33.2
## [25] yaml_2.3.10 S4Arrays_1.7.1
## [27] cytolib_2.19.0 tools_4.4.2
## [29] Rhdf5lib_1.29.0 GenomeInfoDbData_1.2.13
## [31] SummarizedExperiment_1.37.0 BiocGenerics_0.53.3
## [33] buildtools_1.0.0 R6_2.5.1
## [35] matrixStats_1.4.1 stats4_4.4.2
## [37] lifecycle_1.0.4 rhdf5_2.51.0
## [39] zlibbioc_1.52.0 S4Vectors_0.45.2
## [41] flowCore_2.19.0 IRanges_2.41.1
## [43] bslib_0.8.0 data.table_1.16.2
## [45] xfun_0.49 GenomicRanges_1.59.0
## [47] rhdf5filters_1.19.0 sys_3.4.3
## [49] MatrixGenerics_1.19.0 knitr_1.49
## [51] htmltools_0.5.8.1 rmarkdown_2.29
## [53] maketools_1.3.1 compiler_4.4.2- Introduction
- Installation
- Loading the cmapR package
- GCT objects in
R
- Accessing GCT object components
- Parsing GCTX files
- Creating a GCT object from existing workspace objects
- Adding annotations to a GCT object
- Slicing a GCT object
- Melting GCT objects
- Merging two GCT objects
- Math operations on GCT objects
- Writing GCT objects to disk
- Converting GCT objects to SummarizedExperiment objects
- Session Info