readRawInput {ISoLDE} | R Documentation |
Checks and loads into a data.frame
the input file containing
raw allele specific read (ASR) counts so that it can be input into
filterT
.
readRawInput(raw_file, del = "\t", rownames = TRUE, colnames = TRUE)
raw_file |
A character-delimited input file containing raw ASR counts such as described
in |
del |
Specifies the delimiter for the input file, usually a semi-colon ";", a coma "," or a tabulation "\t". (default : "\t"). Note : None of your data values must contain this delimiter (be specially careful in gene names). |
rownames |
Specifies if the file contains some row names to consider. Possible values: TRUE or FALSE (default: TRUE). |
colnames |
Specifies if the file contains some column names to consider. Possible values: TRUE or FALSE (default: TRUE). |
Raw ASR counts are only required for the filtering step (with the
filterT
function) in case the normalized data do not contain 0
counts anymore.
If you do not want to perform the filtering step or if you still have 0 counts
in your normalized file, you do not need to load raw ASR counts.
(For simplicity purpose, we call '0 count' any value of zero in a count file).
A data.frame
containing raw ASR counts from your input file.
Marine Rohmer marine.rohmer@mgx.cnrs.fr,
Christelle Reynès christelle.reynes@igf.cnrs.fr
rawASRcounts_file.txt
: the raw ASR count file on which to run the
readRawInput
function.
readNormInput
: a similar function for normalized ASR count file.
# character-delimited input file containing raw ASR counts rawfile <- system.file("extdata", "rawASRcounts_file.txt", package = "ISoLDE") # loading it into a data.frame using the readRawInput function nbread <- readRawInput(raw_file = rawfile, del = "tab", rownames = TRUE, colnames = TRUE)