Package 'CTexploreR' reference manual

Title:	Explores Cancer Testis Genes
Description:	The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.
Authors:	Axelle Loriot [aut, cre] , Julie Devis [aut] , Anna Diacofotaki [ctb], Charles De Smet [ths], Laurent Gatto [aut, ths]
Maintainer:	Axelle Loriot <[email protected]>
License:	Artistic-2.0
Version:	1.1.0
Built:	2024-06-30 03:29:44 UTC
Source:	https://github.com/bioc/CTexploreR

Gene expression in CCLE Tumors

Description

Plots an expression heatmap of genes in CCLE tumor cell lines.

Usage

CCLE_expression(
  genes = NULL,
  type = NULL,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)
CCLE_expression(
  genes = NULL,
  type = NULL,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)

Arguments

`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`type`	`character()` describing the tumor cell line(s) type to be plotted. Allowed cell lines are "Ovarian", "Leukemia", "Colorectal", "Skin", "Lung", "Bladder", "Kidney", "Breast", "Pancreatic", "Myeloma", "Brain", "Sarcoma", "Lymphoma", "Bone", "Neuroblastoma", "Gastric", "Uterine", "Head_and_Neck", "Bile_Duct" and "Esophageal".
`units`	`character(1)` with expression values unit. Can be "TPM" (default) or "log_TPM" (log(TPM + 1))
`values_only`	`logical(1)`. If `TRUE`, values are returned instead of the heatmap (`FALSE` by default).

Value

A heatmap of selected genes in CCLE cell lines from specified type. If values_only is TRUE, expression values are returned instead.

Examples

## Not run: 
CCLE_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "MAGEA10"),
    type = c("Skin", "Lung"), units = "log_TPM")

## End(Not run)
## Not run: 
CCLE_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "MAGEA10"),
    type = c("Skin", "Lung"), units = "log_TPM")

## End(Not run)

Check spelling of entered variables

Description

Checks the spelling of a vector of entered variable(s) comparing it to a vector of valid names, and removes the ones that are absent from the vector of valid names.

Usage

check_names(variable, valid_vector)
check_names(variable, valid_vector)

Arguments

`variable`	`character()` containing the names of variables to check.
`valid_vector`	`character()` with valid variable names.

Value

A character with valid variables.

Examples

CTexploreR:::check_names(
    variable = c("Ovarian", "leukemia", "wrong_name"),
    valid_vector = c("ovarian", "leukemia")
)
CTexploreR:::check_names(
    variable = c("Ovarian", "leukemia", "wrong_name"),
    valid_vector = c("ovarian", "leukemia")
)

Gene correlations in CCLE cancer cell lines

Description

A function that uses expression data from CCLE cell lines and highlights genes correlated (or anti-correlated) with specified CT gene. Genes with a correlation coefficient above threshold are colored in red if they are CT genes or in blue, if not.

Usage

CT_correlated_genes(gene, corr_thr = 0.5, values_only = FALSE)
CT_correlated_genes(gene, corr_thr = 0.5, values_only = FALSE)

Arguments

`gene`	CT gene selected
`corr_thr`	`numeric(1)` with default 0.5. Genes with an absolute correlation coefficient (Pearson) higher than this threshold will be highlighted.
`values_only`	`logical(1)`, `FALSE` by default. If `TRUE`, the function will return the correlation coefficients with all genes instead of the plot.

Value

A plot where each dots represent the correlation coefficients (Pearson) between genes and the specified CT gene (entered as input). Genes with a correlation coefficient above threshold are colored in red if they are CT genes or in blue, if not. If values_only = TRUE, all correlations coefficients are returned instead.

Examples

## Not run: 
CT_correlated_genes(gene = "MAGEA3")

## End(Not run)
## Not run: 
CT_correlated_genes(gene = "MAGEA3")

## End(Not run)

CT genes description table

Description

Cancer-Testis (CT) genes description, imported from CTdata

Usage

CT_genes
CT_genes

Format

A tibble object with 298 rows and 36 columns.

Rows correspond to CT genes
Columns give CT genes characteristics

Details

See CTdata::CT_genes documentation for details

Value

A tibble of all 298 CT genes with their characteristics

Source

See scripts/make_CT_genes.R in CTdata for details on how this list of curated CT genes was created.

Examples

CT_genes

CT_genes

Gene expression in cells treated or not by a demethylating agent

Description

Plots a heatmap of normalised gene counts (log-transformed) in a selection of cells treated or not by 5-Aza-2'-Deoxycytidine (DAC), a demethylating agent.

Usage

DAC_induction(genes = NULL, multimapping = TRUE, values_only = FALSE)
DAC_induction(genes = NULL, multimapping = TRUE, values_only = FALSE)

Arguments

`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`multimapping`	`logical(1)` defining whether to use multi-mapped gene expression dataset `CTdata::DAC_treated_cells_multimapping` or `DAC_treated_cells`. Default is `TRUE`.
`values_only`	`logical(1)`. If `TRUE`, the function will return the gene normalised logcounts in all samples instead of the heatmap. Default is `FALSE`.

Details

RNAseq data from cells treated or not with 5-aza downloaded from SRA. (SRA references and information about cell lines and DAC treatment are stored the colData of DAC_treated_cells). Data was processed using a standard RNAseq pipeline. hisat2 was used to align reads to grch38 genome. featurecounts was used to assign reads to genes. Note that -M parameter was used or not to allow or not counting multi-mapping reads.

Value

A heatmap of selected genes in cells treated or not by a demethylating agent. If values_only is TRUE, gene normalised logcounts are returned instead.

Examples

DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A"))
DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A",
    multimapping = FALSE))
DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A"))
DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A",
    multimapping = FALSE))

Gene expression in normal tissues (GTEx)

Description

Plots an expression heatmap of genes in normal tissues (GTEx database).

Usage

GTEX_expression(genes = NULL, units = c("TPM", "log_TPM"), values_only = FALSE)
GTEX_expression(genes = NULL, units = c("TPM", "log_TPM"), values_only = FALSE)

Arguments

`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`units`	`character(1)` with expression values unit. Can be `"TPM"` (default) or `"log_TPM"` (log(TPM + 1)).
`values_only`	`logical(1)`. If `TRUE`, the function will return the expression values in all samples instead of the heatmap. Default is `FALSE`.

Value

A heatmap of selected genes expression in normal tissues. If values_only = TRUE, expression values are returned instead.

Examples

GTEX_expression(units = "log_TPM")
GTEX_expression(genes = c("MAGEA1", "MAGEA3"), units = "log_TPM")
GTEX_expression(units = "log_TPM")
GTEX_expression(genes = c("MAGEA1", "MAGEA3"), units = "log_TPM")

Gene expression in different human cell types

Description

Plots a heatmap of genes expression in the different human cell types based on scRNAseq data obtained from the Human Protein Atlas (https://www.proteinatlas.org)

Usage

HPA_cell_type_expression(
  genes = NULL,
  units = c("scaled", "TPM", "log_TPM"),
  scale_lims = NULL,
  values_only = FALSE
)
HPA_cell_type_expression(
  genes = NULL,
  units = c("scaled", "TPM", "log_TPM"),
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`units`	`character(1)` with expression values unit. Can be `"TPM"`, `"log_TPM"` (log(TPM + 1)) or `"scaled"` (scaled TPM values). Default is `"scaled"`.
`scale_lims`	`⁠vector of length 2⁠` setting the lower and upper limits of the heatmap colorbar.
`values_only`	`logical(1)`. If `TRUE`, the function will return the SummarizedExperiment instead of the heatmap. Default is `FALSE`.

Value

A heatmap of selected CT genes expression in different human cell types. If values_only = TRUE, a SummarizedExperiment instead of the heatmap is returned instead.

Examples


HPA_cell_type_expression(
    genes = NULL, units = "scaled", scale_lims = NULL,
    values_only = FALSE)
HPA_cell_type_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4"),
    units = "TPM", scale_lims = c(0, 50),
    values_only = FALSE)
HPA_cell_type_expression(
    genes = NULL, units = "scaled", scale_lims = NULL,
    values_only = FALSE)
HPA_cell_type_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4"),
    units = "TPM", scale_lims = c(0, 50),
    values_only = FALSE)

Expression values (TPM) of genes in normal tissues with or without multimapping

Description

Plots a heatmap of gene expression values in a set of normal tissues. Expression values (in TPM) have been evaluated by either counting or discarding multi-mapped reads. Indeed, many CT genes belong to gene families from which members have identical or nearly identical sequences. Some CT can only be detected in RNAseq data in which multimapping reads are not discarded.

Usage

normal_tissue_expression_multimapping(
  genes = NULL,
  multimapping = TRUE,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)
normal_tissue_expression_multimapping(
  genes = NULL,
  multimapping = TRUE,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)

Arguments

`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`multimapping`	`logical(1)` that specifies if returned expression values must take into account or not multi-mapped reads. TRUE by default.
`units`	`character(1)` with expression values unit. Can be `"TPM"` (default) or `"log_TPM"` (log(TPM + 1)).
`values_only`	`logical(1)`. If `TRUE`, the function will return the expression values in all samples instead of the heatmap. Default is `FALSE`.

Details

RNAseq data from a set of normal tissues were downloaded from Encode. (see inst/scripts/make_CT_normal_tissues_multimapping.R for fastq references) Fastq files were processed using a standard RNAseq pipeline including FastQC for the quality control of the raw data, and trimmomatic to remove low quality reads and trim the adapter from the sequences. hisat2 was used to align reads to grch38 genome. featurecounts was used to assign reads to genes using Homo_sapiens.GRCh38.105.gtf.

Two different pipelines were run in order to remove or not multi-mapping reads. When multimapping was allowed, hisat2 was run with -k 20 parameter (reports up to 20 alignments per read), and featurecounts was run with -M parameter (multi-mapping reads are counted).

Value

A heatmap of selected gene expression values in a set of normal tissues calculated by counting or discarding multi-mapped reads. If values_only = TRUE, gene expression values are returned instead.

Examples

normal_tissue_expression_multimapping(
    genes = c("GAGE13", "CT45A6", "NXF2", "SSX2", "CTAG1A",
    "MAGEA3", "MAGEA6"), multimapping = FALSE)
normal_tissue_expression_multimapping(
    genes = c("GAGE13", "CT45A6", "NXF2", "SSX2", "CTAG1A",
    "MAGEA3", "MAGEA6"), multimapping = TRUE)
normal_tissue_expression_multimapping(
    genes = c("GAGE13", "CT45A6", "NXF2", "SSX2", "CTAG1A",
    "MAGEA3", "MAGEA6"), multimapping = FALSE)
normal_tissue_expression_multimapping(
    genes = c("GAGE13", "CT45A6", "NXF2", "SSX2", "CTAG1A",
    "MAGEA3", "MAGEA6"), multimapping = TRUE)

Promoter methylation of Cancer-Testis genes in normal tissues

Description

Plots a heatmap of mean promoter methylation levels of Cancer-Testis (CT) genes in normal tissues. Methylation levels in tissues correspond to the mean methylation of CpGs located in range of 1000 pb upstream and 200 pb downstream from gene TSS.

Usage

normal_tissues_mean_methylation(
  genes = NULL,
  values_only = FALSE,
  na.omit = TRUE
)
normal_tissues_mean_methylation(
  genes = NULL,
  values_only = FALSE,
  na.omit = TRUE
)

Arguments

`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`values_only`	`logical(1)`, `FALSE` by default. If `TRUE`, the function will return the methylation values in all samples instead of the heatmap.
`na.omit`	`logical(1)` specifying if genes with missing methylation values in some tissues should be removed (`TRUE` by default). Note that no gene clustering will be done when methylation values are missing.

Value

Heatmap of mean promoter methylation of Cancer-Testis (CT) genes in normal tissues. If values_only = TRUE, methylation values are returned instead.

Examples

normal_tissues_mean_methylation()
normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"))
normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"),
    na.omit = FALSE)
normal_tissues_mean_methylation()
normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"))
normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"),
    na.omit = FALSE)

Methylation of CpGs located in Cancer-Testis promoters in normal tissues

Description

Plots a heatmap of the methylation of CpGs located in a Cancer-Testis (CT) promoter, in normal tissues. X-axis corresponds to the CpGs position (related to TSS).

Usage

normal_tissues_methylation(
  gene,
  nt_up = 1000,
  nt_down = 200,
  values_only = FALSE
)
normal_tissues_methylation(
  gene,
  nt_up = 1000,
  nt_down = 200,
  values_only = FALSE
)

Arguments

`gene`	Name of selected CT gene
`nt_up`	Number of nucleotides upstream the TSS to analyse (by default 1000, maximum value 5000)
`nt_down`	Number of nucleotides downstream the TSS to analyse (by default 200, maximum value 5000)
`values_only`	Boolean (FALSE by default). If set to TRUE, the function will return the methylation values of all cytosines in the promoter instead of the heatmap.

Value

Heatmap of the methylation of CpGs located in a Cancer-Testis (CT) promoter, in normal tissues. If values_only = TRUE, methylation values are returned instead.

Examples

normal_tissues_methylation(gene = "TDRD1", 1000, 0)
normal_tissues_methylation(gene = "TDRD1", 1000, 0)

Prepare methylation and expression data of a gene in TCGA tumors

Description

Creates a Dataframe giving for each TCGA sample, the methylation level of a gene (mean methylation of probes located in its promoter) and the expression level of the gene (TPM value).

Usage

prepare_TCGA_methylation_expression(
  tumor = "all",
  gene = NULL,
  nt_up = NULL,
  nt_down = NULL,
  include_normal_tissues = FALSE
)
prepare_TCGA_methylation_expression(
  tumor = "all",
  gene = NULL,
  nt_up = NULL,
  nt_down = NULL,
  include_normal_tissues = FALSE
)

Arguments

`tumor`	`character` defining the TCGA tumor type. Can be one of "SKCM", "LUAD", "LUSC", "COAD", "ESCA", "BRCA", "HNSC", or "all" (default).
`gene`	`character` selected CT gene.
`nt_up`	`numeric(1)` indicating the number of nucleotides upstream the TSS to define the promoter region (1000 by default)
`nt_down`	`numeric(1)` indicating the number of nucleotides downstream the TSS to define the promoter region (200 by default)
`include_normal_tissues`	`logical(1)`. If `TRUE`, the function will include normal peritumoral tissues in addition to tumoral samples. Default is `FALSE`.

Value

a Dataframe giving for each TCGA sample, the methylation level of a gene (mean methylation of probes located in its promoter) and the expression level of the gene (TPM value). The number of probes used to estimate the methylation level is also reported.

Examples

## Not run: 
  CTexploreR:::prepare_TCGA_methylation_expression("LUAD", gene = "TDRD1")

## End(Not run)
## Not run: 
  CTexploreR:::prepare_TCGA_methylation_expression("LUAD", gene = "TDRD1")

## End(Not run)

Determine font size

Description

Gives the fontsize to use for the heatmap based on the matrix's dimension.

Usage

set_fontsize(matrix)
set_fontsize(matrix)

Arguments

matrix

matrix containing the data to visualise

Value

A logical number that is the fontsize to use

Examples

CTexploreR:::set_fontsize(matrix(1:3, 9,8))
CTexploreR:::set_fontsize(matrix(1:3, 9,8))

Subset databases

Description

Check the presence of the genes in the database then subsets the database to only keep these genes' data.

Usage

subset_database(variable = NULL, data)
subset_database(variable = NULL, data)

Arguments

`variable`	`character()` containing the names genes to keep in the data
`data`	`⁠Summarized Experiment⁠` or `SingleCellExperiment` object with valid variable names.

Value

A ⁠Summarized Experiment⁠ or SingleCellExperiment object with only the variables data

Examples


  CTexploreR:::subset_database(variable = "MAGEA1", data = CTdata::GTEX_data())
CTexploreR:::subset_database(variable = "MAGEA1", data = CTdata::GTEX_data())

Gene expression in TCGA tumors

Description

Plots a heatmap of genes expression in TCGA samples (peritumoral and tumor samples when a specific tumor type is specified, or tumor samples only when tumor option is set to "all")

Usage

TCGA_expression(
  tumor = "all",
  genes = NULL,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)
TCGA_expression(
  tumor = "all",
  genes = NULL,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)

Arguments

`tumor`	`character` defining the TCGA tumor type. Can be one of "SKCM", "LUAD", "LUSC", "COAD", "ESCA", "BRCA", "HNSC", or "all" (default).
`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`units`	`character(1)` with expression values unit. Can be `"TPM"` (default) or `"log_TPM"` (log(TPM + 1)).
`values_only`	`logical(1)`. If `TRUE`, the function will return the expression values in all samples instead of the heatmap. Default is `FALSE`.

Value

A heatmap of selected CT genes expression in TCGA samples. If values_only = TRUE, TPM expression data is returned instead.

Examples

## Not run: 
TCGA_expression(
    tumor = "LUAD", genes = c("MAGEA1", "MAGEA3"),
    units = "log_TPM")

## End(Not run)
## Not run: 
TCGA_expression(
    tumor = "LUAD", genes = c("MAGEA1", "MAGEA3"),
    units = "log_TPM")

## End(Not run)

Methylation-Expression correlation of Cancer-Testis genes in TCGA samples

Description

Plots the correlation between methylation and expression values of a Cancer-Testis (CT) gene in TCGA samples.

Usage

TCGA_methylation_expression_correlation(
  tumor = "all",
  gene = NULL,
  nt_up = 1000,
  nt_down = 200,
  min_probe_number = 3,
  include_normal_tissues = FALSE,
  values_only = FALSE
)
TCGA_methylation_expression_correlation(
  tumor = "all",
  gene = NULL,
  nt_up = 1000,
  nt_down = 200,
  min_probe_number = 3,
  include_normal_tissues = FALSE,
  values_only = FALSE
)

Arguments

`tumor`	`character` defining the TCGA tumor type. Can be one of "SKCM", "LUAD", "LUSC", "COAD", "ESCA", "BRCA", "HNSC", or "all" (default).
`gene`	`character` selected gene.
`nt_up`	`numeric(1)` indicating the number of nucleotides upstream the TSS to define the promoter region (1000 by default)
`nt_down`	`numeric(1)` indicating the number of nucleotides downstream the TSS to define the promoter region (200 by default)
`min_probe_number`	`numeric(1)` indicating the minimum number of probes (with methylation values) within the selected region to calculate its mean methylation level. Default is 3.
`include_normal_tissues`	`logical(1)`. If `TRUE`, the function will include normal peritumoral tissues in addition to tumoral samples. Default is `FALSE`.
`values_only`	`logical(1)`. If `TRUE`, the function will return the methylation and expression values in TCGA samples instead of the heatmap. Default is `FALSE`.

Details

The coefficient of correlation is set to NA if no probes are found in promoter regions or if less than 1% of tumors are positive (TPM >= 1) for the gene.

Value

A scatter plot representing for each TCGA sample, gene expression and mean methylation values of probe(s) located in its promoter region (defined as 1000 nucleotides upstream TSS and 200 nucleotides downstream TSS by default). If values_only = TRUE, methylation and expression values are returned in a tibble instead.

Examples

## Not run: 
TCGA_methylation_expression_correlation("LUAD", gene = "TDRD1")

## End(Not run)
## Not run: 
TCGA_methylation_expression_correlation("LUAD", gene = "TDRD1")

## End(Not run)

Gene expression in testis cells

Description

Plots a heatmap of genes expression in the different types of testis cells, using scRNAseq data from "The adult human testis transcriptional cell atlas" (Guo et al. 2018)

Usage

testis_expression(
  cells = c("all", "germ_cells", "somatic_cells", "SSC", "Spermatogonia",
    "Early_spermatocyte", "Late_spermatocyte", "Round_spermatid", "Elongated_spermatid",
    "Sperm1", "Sperm2", "Macrophage", "Endothelial", "Myoid", "Sertoli", "Leydig"),
  genes = NULL,
  scale_lims = NULL,
  values_only = FALSE
)
testis_expression(
  cells = c("all", "germ_cells", "somatic_cells", "SSC", "Spermatogonia",
    "Early_spermatocyte", "Late_spermatocyte", "Round_spermatid", "Elongated_spermatid",
    "Sperm1", "Sperm2", "Macrophage", "Endothelial", "Myoid", "Sertoli", "Leydig"),
  genes = NULL,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

`cells`	`character` defining the testis cell types to be plotted. Can be "germ_cells", "somatic_cells", "all" (default), or any or a combination of "SSC", "Spermatogonia", "Early_spermatocyte", "Late_spermatocyte", "Round_spermatid", "Elongated_spermatid", "Sperm1", "Sperm2", "Macrophage", "Endothelial", "Myoid", "Sertoli", "Leydig".
`genes`	`character` nameing the selected genes. The default value, `NULL`, takes all CT genes.
`scale_lims`	`⁠vector of length 2⁠` setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.
`values_only`	`logical(1)`. If `TRUE`, the function will return the SingleCellExperiment instead of the heatmap. Default is `FALSE`.

Value

A heatmap of selected CT genes expression in single cells from adult testis. If values_only = TRUE, a SingleCellExperiment instead of the heatmap is returned instead.

Examples

## Not run: 
testis_expression(cells = "germ_cells",
                  genes = c("MAGEA1", "MAGEA3", "MAGEA4"))

## End(Not run)
## Not run: 
testis_expression(cells = "germ_cells",
                  genes = c("MAGEA1", "MAGEA3", "MAGEA4"))

## End(Not run)

Package 'CTexploreR'

Help Index

Gene expression in CCLE Tumors

Description

Usage

Arguments

Value

Examples

Check spelling of entered variables

Description

Usage

Arguments

Value

Examples

Gene correlations in CCLE cancer cell lines

Description

Usage

Arguments

Value

Examples

CT genes description table

Description

Usage

Format

Details

Value

Source

Examples

Gene expression in cells treated or not by a demethylating agent

Description

Usage

Arguments

Details

Value

Examples

Gene expression in normal tissues (GTEx)

Description

Usage

Arguments

Value

Examples

Gene expression in different human cell types

Description

Usage

Arguments

Value

Examples

Expression values (TPM) of genes in normal tissues with or without multimapping

Description

Usage

Arguments

Details

Value

Examples

Promoter methylation of Cancer-Testis genes in normal tissues

Description

Usage

Arguments

Value

Examples

Methylation of CpGs located in Cancer-Testis promoters in normal tissues

Description

Usage

Arguments

Value

Examples

Prepare methylation and expression data of a gene in TCGA tumors

Description

Usage

Arguments

Value

Examples

Determine font size

Description

Usage

Arguments

Value

Examples

Subset databases

Description