nonOverlapRNAseq {nanotatoR} | R Documentation |
Extract Read counts for genes that are near SVs.
nonOverlapRNAseq( gnsNonOverlap, SVID, RNASeqData, pattern_Proband = NA, pattern_Mother = NA, pattern_Father = NA )
gnsNonOverlap |
character. genes that are upstream and/or downstream of SV. |
SVID |
character. ID of the SVs. |
RNASeqData |
character. Expression of the genes. |
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. |
Text or Dataframe containing TPM read counts of genes in the family.
RNASeqDir = system.file("extdata", package="nanotatoR") returnMethod="dataFrame" datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir, returnMethod = returnMethod) gnsNonOverlap <- c("DDX11L1", "MIR1302-2HG", "OR4G4P") SVID = 397 datgnnonovrlap <- nonOverlapRNAseq(gnsNonOverlap = gnsNonOverlap, SVID = SVID, RNASeqData = datRNASeq, pattern_Proband = "*_P_*")