Computes and returns NanoString quality control metrics and flags.
Usage
NanoStringQC(raw, exp, detect = 80, sn = 150)
Value
data frame of annotations updated with normalization parameters
Arguments
raw
data frame of raw counts obtained from nCounter (rows represent
genes, columns represent samples). The first three columns must be labeled:
c("Code.Class", "Name", "Accession") and contain that information.
exp
data frame of annotations with rows in the same order as the
columns of raw. Requires a column labeled "File.Name" with entries
corresponding to sample names in raw, also needs columns
c("fov.counted", "fov.count", "binding.density").These fields can be
extracted from the nanostring RCC files.
detect
threshold of percentage of genes expressed over limit of
detection (LOD) that we would like to detect (not decimal), defaults to 80
percent.
sn
signal to noise ratio of the housekeeping genes we are willing to
tolerate, defaults to 150.