Description Usage Arguments Value
Read Pathoscope output
1 2 3 | read_pathoscope(dir_file = ".", s_list = NULL,
smeta_file = "sample_metadata.csv", is.dir = 1, pattern0 = "",
pattern1 = ".tsv", splitPoint = "[.]")
|
dir_file |
path for the directory with all sample files |
s_list |
a list of all the sample IDs involved in the experiment |
smeta_file |
a csv/tsv file containing the sample meta data |
is.dir |
a flag parameter, if the "dir_file" parameter is a directory(1) or a file (0) |
pattern0 |
& pattern1 these are the pattern of strings before and after the sample IDs |
splitPoint |
the character that is used to split words in file names |
A list of "Count data matrix" and "Sample metadata data frame" and the "TaxIDs for the OTUs"
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