QC metrics for NanoString Data

Computes and returns NanoString quality control metrics and flags.

Usage

NanoStringQC(raw, exp, detect = 80, sn = 150)

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.

Value

data frame of annotations updated with normalization parameters

Author

Aline Talhouk, Derek Chiu

Examples

exp.OVD <- subset(expQC, OVD == "Yes")
expOVD <- NanoStringQC(ovd.r, exp.OVD)