Description Usage Arguments Value Examples
The ASExons functions alternatively spliced exons from the exon scores and array scores. It filters probesets on their exon scores, adjusts p-values for multiplicity and only keeps the significant probesets.
1 2 3 |
ExonScores |
The path to the file with the exon scores of the probe sets. |
ArrayScores |
The path to the file with the array scores of the probe sets. |
Exonthreshold |
The exon score threshold to be maintained. If not NULL, probe sets with an exon score lower than this value are not considered further and the p-values will be adjusted for multiplicity after testing. If NULL, all probesets are considered and a multiplicity correction is not performed. |
Groups |
A list with elements specifying the columns of the data in each group. |
paired |
Logical. Are the groups paired? If TRUE the mean paired differences are calculated and tested whether these are significantly different from zero or not. |
significancelevel |
The significance level to be maintained on the p-values. The filtering on the significance is conducted only if an Exonthreshold is specified and the p-value are adjusted for multiplicity. |
Location |
A character string indication the place where the outputs are saved. |
Name |
A character string with the name of the ouput file. Defaults to "REIDSAS". |
A data frame with one line per exon. The columns contain the gene ID, the exon ID, the exon score the test statistic, a p-value and an adjusted p-value. If the groups are paired also the mean paired difference is given. Only the probesets with high enough exon scores and a significant test are kept in the data frame.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## Not run:
data(TC1500264)
PivotTransformData(Data=TC1500264,GeneID=NULL,ExonID=NULL,
REMAPSplitFile="TC1500264_Gene_SplitFile.txt",Location="Output/",Name="TC1500264_Pivot")
REIDSFunction(ASPSR=c(), Indices="Output/TC1500264_LineIndex.csv",
DataFile="Output/TC1500264_Pivot.csv",nsim=50,informativeCalls=FALSE,Summarize=
c("WeightedAll","EqualAll"),rho=0.5,Low_AllSamples=c(),Groups=list(c(1:3),c(4:6)),
Location="Output",Name="TC1500264")
TC1500264_1vs2=ASExons(ExonScores="Output/TC1500264_ExonScores.txt",ArrayScores=
"Output/TC1500264_ArrayScores.txt",Exonthreshold=0.5,Groups=list(c(1:3),c(4:6)),
paired=FALSE,significancelevel=0.05)
## End(Not run)
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