Contents

0.1 Load BiocManager and org.Hs.eg.db

# if (!requireNamespace("BiocManager", quietly = TRUE))
#   install.packages("BiocManager")
# BiocManager::install("org.Hs.eg.db")
library(org.Hs.eg.db)

0.2 Fetch gene symbols

counts=read.delim('/Users/charleenadams/gene_names/logcounts.txt', check.names = FALSE)
head(counts[1:5])
##               45125      45139      45145      45147      45148
## 1          1.190306  0.2323686  0.8670097  0.5811252  0.9980264
## 10        -1.489920 -2.9889655 -2.4913107 -1.7484081 -2.5303738
## 100        2.044132  1.3438087  2.0887313  2.3479979  2.3107896
## 1000       2.261277  1.6633385  3.0446126  0.4893704  2.7625014
## 10000      5.200934  5.5386320  6.1440904  6.4558167  5.4678420
## 100009667  1.190306  0.9327595  0.7373523  0.4893704  1.6495573
ann <- select(org.Hs.eg.db,keys=rownames(counts),columns=c("ENTREZID","SYMBOL","GENENAME"))

head(ann)
##    ENTREZID   SYMBOL                            GENENAME
## 1         1     A1BG              alpha-1-B glycoprotein
## 2        10     NAT2               N-acetyltransferase 2
## 3       100      ADA                 adenosine deaminase
## 4      1000     CDH2                          cadherin 2
## 5     10000     AKT3       AKT serine/threonine kinase 3
## 6 100009667 POU5F1P5 POU class 5 homeobox 1 pseudogene 5

0.3 Rubs: https://rpubs.com/Charleen_D_Adams/754505