Description Usage Arguments Value Author(s) See Also Examples
DESeq1 is a customed way to use DESeq2 package for differencially expression analysis based on raw counts and design object,and create a DESeqList with dds,difSig and siggenes object.
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counts |
raw counts matrix |
design |
design object with sample rows and clinic feature cols |
contrast.col |
the colnames of contrast.Like "N.status" |
count.filter |
the rowmean filter of counts |
cutoff.lFC |
the cutoff of log foldchange |
cutoff.padj |
the cutoff of adjusted P value |
report |
whether to do quality control report.Default is F. |
save.file |
whether to save .rda object for DESeqList |
names |
part name of saved files |
DESeqList
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | library(lucky)
## data preparation
data("rna.counts")
data("rna.design")
counts = rna.counts;rm(rna.counts)
design = rna.design;rm(rna.design)
## DESeq2 package standard pipeline
dl1 <- DESeq1(counts,
design,
contrast.col= "condition",
contrast.level = c("normal","tumor"),
contrast.control = "normal",
count.filter=10,
cutoff.lFC = 2,
cutoff.padj = 0.05,
save.file = F,
names = "love",
report = T)
View(dl1)
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