countTable: Extract count table directly from experiment

In JokingHero/ORFik: Open Reading Frames in Genomics

Extract count table directly from experiment

Description

Used to quickly load pre-created 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, to get default count tables!

Usage

countTable(
  df,
  region = "mrna",
  type = "count",
  collapse = FALSE,
  count.folder = "default"
)

Arguments

df	an ORFik experiment or path to folder with countTable, use path if not same folder as experiment libraries. Will subset to the count tables specified if df is experiment. If experiment has 4 rows and you subset it to only 2, then only those 2 count tables will be outputted.
region	a character vector (default: "mrna"), make raw count matrices of whole mrnas or one of (leaders, cds, trailers).
type	character, default: "count" (raw counts matrix). Which object type and normalization do you want ? "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)
count.folder	character, default "auto" (Use count tables from original bam files stored in "QC_STATS", these are like HTseq count tables). To load your custome count tables from pshifted reads, set to "pshifted" (remember to create the pshifted tables first!). If you have custom ranges, like reads over uORFs stored in a folder called "/uORFs" relative to the bam files, set to "uORFs". Always create these custom count tables with makeSummarizedExperimentFromBam. Always make the location of the folder directly inside the bam file directory!

Details

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, if multiple exist, see if any start with "countTable_", if so, subset. If loaded as SummarizedExperiment or deseq, the colData will be made from ORFik.experiment information.

Value

a data.table/SummarizedExperiment/DESeq object of columns as counts / normalized counts per library, column name is name of library. Rownames must be unique for now. Might change.

See Also

Other countTable: countTable_regions()

Examples

# Make experiment
df <- ORFik.template.experiment()
# Make QC report to get counts ++ (not needed for this template)
# 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")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.