Quick meal prep in R

quickmeal.r

# Get date
date = sapply(strsplit(as.character(Sys.Date()), '-', fixed = T), paste, collapse = "")

## biomart and AnnotationDbi
# Map a gene id to get an ENTREZ id.
require(AnnotationDbi)
require(org.Mm.eg.db) # mice 

entrez = mapIds(org.Mm.eg.db,
                keys=ens_gene, # has to be a vector
                column=c('SYMBOL'),
                keytype='ENTREZID',
                multiVals='first')

# Get biomart
bm = useMart("ENSEMBL_MART_ENSEMBL", "mmusculus_gene_ensembl", host="oct2016.archive.ensembl.org")

# list attributes
a = listAttributes(bm)

# list filters
f= listFilters(bm)

# Shop biomart
bm1 = getBM(attributes = c("ensembl_gene_id", 
                           "chromosome_name", 
                           "start_position", 
                           "end_position", 
                           "percentage_gc_content"),
            mart=bm)


# change multiple columns into factor
df %>% mutate_if(is.character,as.factor)