Description Usage Arguments Details Value Examples
Generate a raw sgRNA read count table from fastq files and an annotation file. The raw count table can be an input of UQnormalize()
to apply sgRSEA()
. Python is required.
1 | sgCount(fqInfo, annotation, seqlen = 20, output_prefix = "sgCount")
|
fqInfo |
A tab-delimited text file. Rows represent fastq files and four cloumns are fastq filename, experimental condition name, starting and ending location of trimming of sgRNA reads. See the example below. |
annotation |
A tab-delimited annotation file. Columns are sgRNA name (1st), gene name (2nd), and sgRNA sequence read (3rd). |
seqlen |
Length of the sgRNA read. |
output_prefix |
A |
This function calls a python code located at system.file(package = "sgRSEA")
.
Generate a tab-delimited file of sgRNA read count table. Columns are sgRNAs, genes and read counts at multiple experimental conditions.
1 2 3 | ## A toy example
## example input files can be found at .libPaths()/sgRSEA/extdata.
## sgCount('fqInfo.txt', 'library2.txt', 20, 'Test')
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