Nothing
## ----install-0, eval=FALSE, echo=TRUE-----------------------------------------
# if(!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
# BiocManager::install("metaseqR2")
## ----load-library, echo=TRUE, eval=TRUE, message=FALSE, warning=FALSE---------
library(metaseqR2)
## ----seed-0, eval=TRUE, echo=TRUE---------------------------------------------
set.seed(42)
## ----data-1, eval=TRUE, echo=TRUE---------------------------------------------
data("mm9GeneData",package="metaseqR2")
## ----head-1, eval=TRUE, echo=TRUE---------------------------------------------
head(mm9GeneCounts)
## ----random-1, eval=TRUE, echo=TRUE-------------------------------------------
sampleListMm9
## ----random-2, eval=TRUE, echo=TRUE-------------------------------------------
libsizeListMm9
## ----example-1, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE----
library(metaseqR2)
data("mm9GeneData",package="metaseqR2")
# You can explore the results in the session's temporary directory
print(tempdir())
result <- metaseqr2(
counts=mm9GeneCounts,
sampleList=sampleListMm9,
contrast=c("adult_8_weeks_vs_e14.5"),
libsizeList=libsizeListMm9,
annotation="embedded",
embedCols=list(
idCol=4,
gcCol=5,
nameCol=8,
btCol=7
),
org="mm9",
countType="gene",
normalization="edger",
statistics="edger",
pcut=0.05,
qcPlots=c(
"mds","filtered","correl","pairwise","boxplot","gcbias",
"lengthbias","meandiff","meanvar","deheatmap","volcano",
"mastat"
),
figFormat=c("png","pdf"),
exportWhat=c("annotation","p_value","adj_p_value","fold_change"),
exportScale=c("natural","log2"),
exportValues="normalized",
exportStats=c("mean","sd","cv"),
exportWhere=file.path(tempdir(),"test1"),
restrictCores=0.1,
geneFilters=list(
length=list(
length=500
),
avgReads=list(
averagePerBp=100,
quantile=0.25
),
expression=list(
median=TRUE,
mean=FALSE,
quantile=NA,
known=NA,
custom=NA
),
biotype=getDefaults("biotypeFilter","mm9")
),
outList=TRUE
)
## ----head-2, eval=TRUE, echo=TRUE---------------------------------------------
head(result[["data"]][["adult_8_weeks_vs_e14.5"]])
## ----example-2, eval=TRUE, echo=TRUE, tidy=FALSE, message=FALSE, warning=FALSE----
library(metaseqR2)
data("mm9GeneData",package="metaseqR2")
result <- metaseqr2(
counts=mm9GeneCounts,
sampleList=sampleListMm9,
contrast=c("adult_8_weeks_vs_e14.5"),
libsizeList=libsizeListMm9,
annotation="embedded",
embedCols=list(
idCol=4,
gcCol=5,
nameCol=8,
btCol=7
),
org="mm9",
countType="gene",
whenApplyFilter="prenorm",
normalization="edaseq",
statistics=c("deseq","edger"),
metaP="fisher",
#qcPlots=c(
# "mds","biodetection","countsbio","saturation","readnoise","filtered",
# "correl","pairwise","boxplot","gcbias","lengthbias","meandiff",
# "meanvar","rnacomp","deheatmap","volcano","mastat","biodist","statvenn"
#),
qcPlots=c(
"mds","filtered","correl","pairwise","boxplot","gcbias",
"lengthbias","meandiff","meanvar","deheatmap","volcano",
"mastat"
),
restrictCores=0.1,
figFormat=c("png","pdf"),
preset="medium_normal",
exportWhere=file.path(tempdir(),"test2"),
outList=TRUE
)
## ----example-3, eval=TRUE, echo=TRUE, tidy=FALSE, message=FALSE, warning=FALSE----
library(metaseqR2)
data("mm9GeneData",package="metaseqR2")
result <- metaseqr2(
counts=mm9GeneCounts,
sampleList=sampleListMm9,
contrast=c("adult_8_weeks_vs_e14.5"),
libsizeList=libsizeListMm9,
annotation="embedded",
embedCols=list(
idCol=4,
gcCol=5,
nameCol=8,
btCol=7
),
org="mm9",
countType="gene",
normalization="edaseq",
statistics=c("deseq","edger"),
metaP="fisher",
qcPlots=c(
"mds","filtered","correl","pairwise","boxplot","gcbias",
"lengthbias","meandiff","meanvar","deheatmap","volcano",
"mastat"
),
restrictCores=0.1,
figFormat=c("png","pdf"),
preset="medium_normal",
outList=TRUE,
exportWhere=file.path(tempdir(),"test3")
)
## ----example-4, eval=TRUE, echo=TRUE, tidy=FALSE, message=FALSE, warning=FALSE----
library(metaseqR2)
data("mm9GeneData",package="metaseqR2")
result <- metaseqr2(
counts=mm9GeneCounts,
sampleList=sampleListMm9,
contrast=c("adult_8_weeks_vs_e14.5"),
libsizeList=libsizeListMm9,
annotation="embedded",
embedCols=list(
idCol=4,
gcCol=5,
nameCol=8,
btCol=7
),
org="mm9",
countType="gene",
normalization="edaseq",
statistics=c("edger","limma"),
metaP="fisher",
figFormat="png",
preset="medium_basic",
qcPlots=c(
"mds","filtered","correl","pairwise","boxplot","gcbias",
"lengthbias","meandiff","meanvar","deheatmap","volcano",
"mastat"
),
restrictCores=0.1,
outList=TRUE,
exportWhere=file.path(tempdir(),"test4")
)
## ----example-5, eval=TRUE, echo=TRUE, tidy=FALSE, message=FALSE, warning=FALSE----
data("mm9GeneData",package="metaseqR2")
weights <- estimateAufcWeights(
counts=as.matrix(mm9GeneCounts[,9:12]),
normalization="edaseq",
statistics=c("edger","limma"),
nsim=1,N=10,ndeg=c(2,2),top=4,modelOrg="mm9",
rc=0.1,libsizeGt=1e+5
)
## ----head-3, eval=TRUE, echo=TRUE---------------------------------------------
weights
## ----example-6, eval=TRUE, echo=TRUE, tidy=FALSE, message=FALSE, warning=FALSE----
data("hg19pvalues",package="metaseqR2")
# Examine the data
head(hg19pvalues)
# Now combine the p-values using the Simes method
pSimes <- apply(hg19pvalues,1,combineSimes)
# The harmonic mean method with PANDORA weights
w <- getWeights("human")
pHarm <- apply(hg19pvalues,1,combineHarmonic,w)
# The PANDORA method
pPandora <- apply(hg19pvalues,1,combineWeight,w)
## ----help-2, eval=TRUE, echo=TRUE, message=FALSE------------------------------
help(statEdger)
## ----si-1, eval=TRUE, echo=TRUE-----------------------------------------------
sessionInfo()
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