SVexpression_solo {nanotatoR} | R Documentation |
Annotating the Overlapping and Non-Overlapping genes with RNAseq expression
SVexpression_solo( input_fmt_SV = c("Text", "dataFrame"), smapdata, smappath, input_fmt_RNASeq = c("Text", "dataFrame"), RNASeqData, RNASeqPATH, outputfmt = c("Text", "datFrame"), pattern_Proband = NA, EnzymeType = c("SVMerge", "SE") )
input_fmt_SV |
character. Input format of the SV data.Options "Text" or "DataFrame". |
smapdata |
dataframe. SV data dataframe. |
smappath |
character. smap path. |
input_fmt_RNASeq |
character. Input format of the RNASeq data. Options "Text" or "DataFrame".. |
RNASeqData |
dataFrame. RNAseq data with gene names. |
RNASeqPATH |
character. RNAseq dataset path . |
outputfmt |
character. Output format of the result. Options "Text" or "DataFrame".. |
pattern_Proband |
character. Pattern for proband. |
EnzymeType |
character. Enzyme used. option "SVMerge" or "SE". |
Dataframe Annotated datafreme with RNASeq data.
RNASeqDir = system.file("extdata", package="nanotatoR") returnMethod="dataFrame" datRNASeq <- RNAseqcombine_solo(RNASeqDir = RNASeqDir, returnMethod = returnMethod) smapName="NA12878_DLE1_VAP_solo5.smap" smap = system.file("extdata", smapName, package="nanotatoR") smap = system.file("extdata", smapName, package="nanotatoR") bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR") outpath <- system.file("extdata", package="nanotatoR") datcomp<-overlapnearestgeneSearch(smap = smap, bed=bedFile, inputfmtBed = "bed", outpath, n = 3, returnMethod_bedcomp = c("dataFrame"), input_fmt_SV = "Text", EnzymeType = "SE", bperrorindel = 3000, bperrorinvtrans = 50000) datRNASeq1 <- SVexpression_solo (input_fmt_SV=c("dataFrame"), smapdata = datcomp, input_fmt_RNASeq=c("dataFrame"), RNASeqData = datRNASeq, outputfmt=c("datFrame"), pattern_Proband = "*_P_*", EnzymeType = c("SE")) datRNASeq1[1,]