countTable {ORFik} | R Documentation |
Used to quickly load read count tables to R.
If df is experiment:
Extracts by getting /QC_STATS directory, and searching for region
Requires ORFikQC
to have been run on experiment!
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), "summarized" (SummarizedExperiment object), "deseq" (Deseq2 experiment, design will be all valid non-unique columns except replicates, change by using DESeq2::design, normalization alternatives are: "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 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.
# Make experiment ORFik.template.experiment() # 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) # Get count Table of mrnas as summarizedExperiment # countTable(df, "mrna", type = "summarized") # Get count Table of mrnas as DESeq2 object, # for differential expression analysis # countTable(df, "mrna", type = "deseq")