base_distribution: Create a graphical evaluation of sequencing results

Description Usage Arguments Details Value Examples

View source: R/exported_functions.R

Description

This function creates a graphical evalution of the sequencing results to determine the quality of the created library.

Usage

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base_distribution(input_sequence, ab1file, replacements, trace_cutoff = 80)

Arguments

input_sequence

The sequence which was modified. This is an object of type character containing the sequence.

ab1file

The path to the ab1file which was provided by the sequencer/sequencing service

replacements

The mutations which were desired.

trace_cutoff

The minimal sum of signals (4 nucleotides) for a position in the sequence. [default: 80]

Details

The functions aligns the obtained sequencing results to the target gene sequence. It also tries to align the reverse complement of the obtained sequence. Afterwards it checks for mismatches between the sequences. Mismatches are likely to be sucessfully mutated nucleotides. Positions regarded as mismatches are displayed as pie charts. The shown distributions are based on the signal intensities of the four nucleobases at the mismatch positions. You can compare the pie charts with expected pattern of randomization, therefore validating the quality of the created library.

Value

Plots on the active/default graphics device.

Examples

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## Not run: 
data(MSD_BsaI_setup_lv2)
abfile<-"activesite_for_200718.ab1"
base_distribution(input_sequence=input_sequence, ab1file=abfile, replacements=mutations)

## End(Not run)

ipb-halle/GoldenMutagenesis documentation built on Sept. 1, 2020, 3:24 p.m.