Mercurial > repos > davidecangelosi > pipe_t
changeset 4:e248cd7769e8 draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit fe7763760d58ae2b51441b67162bb5f86cffa91e
| author | davidecangelosi |
|---|---|
| date | Mon, 06 May 2019 06:31:30 -0400 |
| parents | e2fcf5a4609c |
| children | 29a8df9f543d |
| files | pipe-t.R |
| diffstat | 1 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/pipe-t.R Mon May 06 05:54:37 2019 -0400 +++ b/pipe-t.R Mon May 06 06:31:30 2019 -0400 @@ -177,7 +177,7 @@ if (length(n.header)==0) n.header <- 0 # Read data, skip the required lines - out <- read.delim(file=readfile, header=FALSE, colClasses="character", nrows=nspots*n.data[i], skip=n.header, strip.white=TRUE, ...) + out <- read.delim(file=readfile, header=TRUE, colClasses="character", nrows=nspots*n.data[i], skip=n.header-1, strip.white=TRUE, ...) # Return out } # .readCtSDS @@ -256,9 +256,10 @@ } if (missing(column.info)) { column.info <- switch(format, EDS = list(flag="EXPFAIL", feature="Target.Name", position="Well.Position", Ct="CT"), - plain = list(flag = 4, - feature = 6, type = 7, position = 3, Ct = 8), SDS = list(flag = 4, - feature = 6, type = 7, position = 3, Ct = 8), LightCycler = list(feature = "Name", + plain = list(flag = 4, feature = 6, type = 7, position = 3, Ct = 8), + #SDS = list(flag = 4,feature = 6, type = 7, position = 3, Ct = 8), + SDS = list(flag = "Omit",feature = "Detector", type = "Task", position = "Wells", Ct = "Ct"), + LightCycler = list(feature = "Name", position = "Pos", Ct = "Cp"), CFX = list(feature = "Content", position = "Well", Ct = "Cq.Mean"), OpenArray = list(flag = "ThroughHole.Outlier", feature = "Assay.Assay.ID", type = "Assay.Assay.Type",