Updated docs on probe-to-gene mapping

QuackenbushLab · Feb 28, 2025 · 20d1f77 · 20d1f77
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Showing 2 changed files with 6 additions and 13 deletions.
diff --git a/R/NetworkDataCompanion.R b/R/NetworkDataCompanion.R
@@ -302,6 +302,7 @@ NetworkDataCompanion=setRefClass("NetworkDataCompanion",
 
            # Function to map to probes to a gene-level measurement
            # probe_gene_map is in the format output from the mapProbesToGenes function
+           # genesOfInterest is a character vector, one gene per entry
            # not all genesOfInterest need to be in probe_gene_map, but if none are, then this is meaningless
 	         probeToMeanPromoterMethylation = function(methylation_betas,
                                                      probe_gene_map,
@@ -331,12 +332,6 @@ NetworkDataCompanion=setRefClass("NetworkDataCompanion",
                  data.frame(check.names=F)
              }
 
-             # ## split the probe map to a long form where there are multiple genes mapped to the same probe
-             # mappedBetasLong = mappedBetas %>%
-             #   separate_rows(geneNames, sep = ";") %>%
-             #   drop_na(geneNames) %>%
-             #   data.frame(check.names = F)
-
              ## map probe-level methylation to the mean for each gene
              betaMeans = mappedBetasLong %>%
                group_by(geneNames) %>%
@@ -375,12 +370,8 @@ NetworkDataCompanion=setRefClass("NetworkDataCompanion",
              # map methylation to gene level
              # methylation betas should be samples in rows
              # and CGs in columns
-             # luad for testing
-             # methylation_betas = fread("~/Desktop/tcga_luad_methylations.txt",data.table=F)
-             # row.names(methylation_betas) = methylation_betas$probeID
-             # array = "450k"
-
-	     row.names(methylation_betas) = methylation_betas$probeID
+
+             row.names(methylation_betas) = methylation_betas$probeID
 
              geneLevelMeth = methylation_betas %>%
                dplyr::select(-probeID) %>%

diff --git a/man/probeToMeanPromoterMethylation.Rd b/man/probeToMeanPromoterMethylation.Rd
@@ -8,7 +8,9 @@
 \arguments{
   \item{methylation_betas}{A data frame of methylation beta values, with CGs in rows and samples in columns. The first column must be "probeID" and contain the Illumina probeIDs matching the probe_gene_map argument or a subset thereof.}
   \item{probe_gene_map}{Output from mapProbesToGenes, or otherwise a bespoke matrix with four columns: probeID, geneName, ensemblID, distToTSS.}
-  \item{genesOfInterest}{Character vector of gene names for which mean promoter methylation should be calculated.}
+  \item{genesOfInterest}{Character vector of gene names for which mean promoter methylation should be calculated. 
+  Note that each entry in the vector should contain only one gene and that gene should not be repeated in the entry; e.g., \code{c("ASMTL","CRLF2")} is a correct input while \code{c("ASMTL;ASMTL", "CRLF2")} will fail to find probes mapping to ASMTL. 
+  This could happen, for example, if you pull a column of genes from a resource that combines splice variants with a semicolon.}
 }
 
 \value{Matrix of samples in rows and genes in columns. row.names stores sample names and colnames stores gene names.