count_set: Generate a count_set summerized experiment from NanoString...

In MarthaCooper/NanoStringClustR: NanoString data normalization and differential gene expression analysis

Description

Generates a summerized experiment from NanoString count data in an nSolver RCC Collector Tool Format or matrix and (optional) sample annotations including group, batch, and sample pairing.

Usage

count_set(
  rccexp_dir = NULL,
  count_data = NULL,
  group = NULL,
  batch = NULL,
  pair = NULL,
  samp_id = NULL,
  output_log = NULL,
  count_se = NULL,
  low_reps = FALSE,
  verbose = TRUE
)

Arguments

rccexp_dir	Full path to the csv file generated by nSolver RCC Collector Tool Format Export. Default = NULL
count_data	a matrix of count data; genes as rows, samples as columns. Contains 3 columns called "Code_Class", "Gene_Name" & "Accession". Code_class contains probe annotations "Endogenous", "Positive" and "Negative". Default = NULL
group	Biological groups for each lane of counts defined by a factor or vector. Default = NULL
batch	Batch information such as nanostring chip ID, defined by a factor or vector of integers. Default = NULL
pair	Sample pairing defined by a factor or vector. Default = NULL
samp_id	Sample IDs defined by a factor or vector. This is used to build the replicate matrix. Default = NULL
output_log	File path to directory where the summarized experiment will be saved
count_se	File path to an already generated summarized experiment
low_reps	Force Ccount_set to build if a group contains less than 2 replicates. Default = FALSE
verbose	Verbosity ON/OFF. Default = TRUE

Value

A summarized experiment

Examples

# biological groups
rnf5_group <- c(rep("WT", 5), rep("KO", 5))

# sample ids
rnf5_sampleid <- c("GSM3638131", "GSM3638132", "GSM3638133", "GSM3638134",
                  "GSM3638135", "GSM3638136", "GSM3638137", "GSM3638138",
                  "GSM3638139", "GSM3638140")

# build count_set
rnf5_count_set <- count_set(count_data = Rnf5,
                            group = rnf5_group,
                            samp_id = rnf5_sampleid)

MarthaCooper/NanoStringClustR documentation built on June 25, 2021, 9:41 p.m.