countTable {ORFik} | R Documentation |
Used to quickly load read count tables to R.
countTable(df, region = "mrna", type = "count", collapse = FALSE)
df |
an ORFik |
region |
a character vector (default: "mrna"), make raw count matrices of whole mrnas or one of (leaders, cds, trailers). |
type |
default: "count" (raw counts matrix), alternative is "fpkm", "log2fpkm" or "log10fpkm" |
collapse |
a logical/character (default FALSE), if TRUE all samples within the group SAMPLE will be collapsed to one. If "all", all groups will be merged into 1 column called merged_all. Collapse is defined as rowSum(elements_per_group) / ncol(elements_per_group) |
If df is experiment:
Extracts by getting /QC_STATS directory, and searching for region
Requires ORFikQC
to have been run on experiment!
If df is path to folder: Loads the the file in that directory with the regex region.rds, where region is what is defined by argument.
a data.table of columns as counts per library, column name is name of library. Rownames must be unique for now. Might change.
# 1. Pick directory dir <- system.file("extdata", "", package = "ORFik") # 2. Pick an experiment name exper <- "ORFik" # 3. Pick .gff/.gtf location txdb <- system.file("extdata", "annotations.gtf", package = "ORFik") template <- create.experiment(dir = dir, exper, txdb = txdb, viewTemplate = FALSE) template$X5[6] <- "heart" # <- fix non unique row # read experiment df <- read.experiment(template) # Make QC report to get counts ++ # ORFikQC(df) # Get count Table of mrnas # countTable(df, "mrna") # Get count Table of cds # countTable(df, "cds") # Get count Table of mrnas as fpkm values # countTable(df, "mrna", type = "count") # Get count Table of mrnas with collapsed replicates # countTable(df, "mrna", collapse = TRUE)