SVexpression_duo_trio {nanotatoR} | R Documentation |
Extract Read counts for genes that are near or overalapping SVs.
SVexpression_duo_trio( input_fmt_SV = c("Text", "dataFrame"), smapdata, smappath, input_fmt_RNASeq = c("Text", "dataFrame"), RNASeqData, RNASeqPATH, outputfmt = c("Text", "datFrame"), pattern_Proband = NA, pattern_Mother = NA, pattern_Father = NA, EnzymeType = c("SVMerge", "SE") )
input_fmt_SV |
character. genes that are upstream and/or downstream of SV. input_fmt_RNASeq |
smapdata |
dataframe. smap data in dataframe format. |
smappath |
character. smap path. |
input_fmt_RNASeq |
character. input format of RNASEQ data. Text or dataframe. |
RNASeqData |
character. Expression of the genes. |
RNASeqPATH |
character. RNASEQ path. |
outputfmt |
character. Output format choice dataframe or text. |
pattern_Proband |
character. Pattern to identify the proband reads. |
pattern_Mother |
character. Pattern to identify the mother reads. |
pattern_Father |
character. Pattern to identify the father reads. |
EnzymeType |
character. Enzyme used. option "Dual" or "DLE". |
Text or Dataframe containing TPM read counts of genes in the family.
## Not run: RNASeqDir = system.file("extdata", package="nanotatoR") returnMethod="dataFrame" datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir, returnMethod = returnMethod) smapName="NA12878_DLE1_VAP_solo5.smap" smap = system.file("extdata", smapName, package="nanotatoR") datcomp<-overlapnearestgeneSearch(smap = smap, bed=bedFile, inputfmtBed = "BED", outpath, n = 3, returnMethod_bedcomp = c("dataFrame"), input_fmt_SV = "Text", EnzymeType = "SVMerge", bperrorindel = 3000, bperrorinvtrans = 50000) datRNASeq1 <- SVexpression( input_fmt_SV=c("dataFrame"), input_fmt_RNASeq=c("dataFrame"), RNASeqData = datRNASeq, outputfmt=c("datFrame"), pattern_Proband = "*_P_*", EnzymeType = c("SVMerge")) ## End(Not run)