Description Usage Arguments Value
Takes a matrix and filters by counts greater than 10 in filtperc % of SMMART samples
1 2 3 4 5 6 7 8 9 10 | 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
)
|
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 |
list of matrices
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