import_raw_tally: Import raw tally file for processing

In ruy204/FiTnEss: FiTnEss: Finding TnSeq Essential Genes

Description

The function imports raw tally .txt file into the function and start processing.

Usage

import_raw_tally(filename,CIA=TRUE)

Arguments

filename	directory and name for raw tally .txt file, for example: "/folder/raw_tally_rep1.txt"
CIA	gene type, CIA=TRUE only include

Details

The input data needs to be .txt file, with 6 columns: index(row index, or chromosome index), TA_start(start position of TA site), TA_end(end position of TA site), Locus.CIA(gene name), plus_n(number of reads aligned on + strand), minus_n(number of reads aligned on - strand).

For example, raw_tally[1,]

ChrI 3 4 PA14_00010 0 1

Value

Returns a dataframe

Examples

import_raw_tally("/home/TnSeq/data/test_data/PA14_M9_rep1_tally.txt",
                 CIA = TRUE)


{ ~tally_preparation }
{ ~import_file }

ruy204/FiTnEss documentation built on Jan. 23, 2021, 2:52 a.m.