This function creates an object of the parcutils_chip
. parcutils_chip is an extension of the the RangedSummarizedExperiment
.
This object make sure that it contains necessary elements to perform downstream chipseq analysis. Downstream exploratory and visualization functions will be based on this object.
Arguments
- x
a list of the object(s) of
normalisedMatrix
.- row_ranges
an object of the class GenomicRanges. Each range must be identified by an unique id stored in a column
name
,
Value
an object of the class parcutils_chip. Class parcutils_chip extends to RangedSummarizedExperiment. It contains data in the below format
"assay" These is the object of NormalisedMatrix for the sample.
"columns" Columns are the columns in each assays. In this case they are the bins described in NormalisedMatrix.
"rowData" RPM value for each feature (row) across samples.
Examples
signal = GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1, 4, 7, 11, 14, 17, 21, 24, 27),
end = c(2, 5, 8, 12, 15, 18, 22, 25, 28)),
score = c(1, 2, 3, 1, 2, 3, 1, 2, 3))
#> Error in GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 4, 7, 11, 14, 17, 21, 24, 27), end = c(2, 5, 8, 12, 15, 18, 22, 25, 28)), score = c(1, 2, 3, 1, 2, 3, 1, 2, 3)): could not find function "GRanges"
target = GRanges(seqnames = "chr1", ranges = IRanges(start = 10, end = 20), name = "feat_1")
#> Error in GRanges(seqnames = "chr1", ranges = IRanges(start = 10, end = 20), name = "feat_1"): could not find function "GRanges"
x = normalizeToMatrix(signal, target, extend = 10, w = 2)
#> Error in normalizeToMatrix(signal, target, extend = 10, w = 2): could not find function "normalizeToMatrix"
rownames(x) <- "feat_1"
#> Error in rownames(x) <- "feat_1": object 'x' not found
make_parcutils_chip(x, target)
#> Error in .validate_a_list_of_normalised_matrix(x = x): object 'x' not found