normalizeRUV: normalize RUV

In patterja/smmartprediction: SMMART Drug Prediction

Description

Takes a matrix and filters by counts greater than 10 in filtperc % of SMMART samples

Usage

normalizeRUV(
 
    exp_matx = read.csv("/Users/patterja/Box Sync/Heiser_Atwater/SMMART_NORMALIZATION/DATA_MATRICES/PROCESSED/tpm_breast_20190214.txt",
    sep = "\t", row.names = 1),
  includeBCCL = FALSE,
  filtperc = 10,
  mincnt = 3,
  normtype = "NONE",
  setk
)

Arguments

filtperc	(int): 10% of SMMART samples will have counts greater than mincnt
mincnt	(int): TPM use 3, counts to CPM use 10
normtype	(string): "NONE", "CPM"
setk	(numeric): number of factors to remove. if includeBCCL=T use CPM, setk=7, filtperc=10, mincnt = 10, if includeBCCL=F use TPM, setk=1, filtperc=10, mincnt = 3,
exp_matx:	matrix of expression, rownames=genes
includeBCCL:	TRUE OR FALSE

Value

list of matrices

patterja/smmartprediction documentation built on Oct. 10, 2020, 3:35 p.m.