Updated Data Formatting

[zohaib-a-ahmed]

Clients introduced a new data format that MeltShiny is going to operate from named as AYGU-1_MeltR that should be used going forward.

This will require rewriting some buried architecture regarding formatting the data going into the MeltR package, which is currently throwing internal errors (within MeltR package). Something is incorrectly being passed into the library post data upload.

This bug needs to be addressed before the application can be used with the new csv format.

[adhampton110]

/cc @zohaib-a-ahmed @Massi-Papi @ethan-gray-01 @LikhitaPulijala @BollepalliPranitha @kungfuchicken

It appears there are two options going forward. Does the end user wish to pursue either of these options:

1. Support for both formats: old (test.csv) & new (AYGU-1_MeltR.csv)
2. Support for the New Format Only: (AYGU-1_MeltR.csv)

[adhampton110]

For testing purposes, when using AYGU-1_MeltR.csv as the dataset file, what should be the values for the following fields?:

• Sample number of blank
• Select the wavelength
• Enter the temperature used to calculate the concentration with Beers law
• Specify necelic acid type
• Specify sequences
• Decide if you wan to have the molar extinction coefficients calculated or provide them manually
• Optional methods
• Choose a Tm method
• Select the molecular state

[adhampton110]

@BollepalliPranitha Did you merge #183 by accident?

[BollepalliPranitha]

@adhampton110
I merged the PR and thought of creating the new issue for the bug . But I found that the issue found is working with test.csv, so I reverted back the changes .
so those changes were not in the main
You can work on the bug and make the necessary changes

[adhampton110]

For testing purposes, when using AYGU-1_MeltR.csv as the dataset file, what should be the values for the following fields?:

• Sample number of blank
• Select the wavelength
• Enter the temperature used to calculate the concentration with Beers law
• Specify nucleic acid type
• Specify sequences
• Decide if you wan to have the molar extinction coefficients calculated or provide them manually
• Optional methods
• Choose a Tm method
• Select the molecular state

Could we get confirmation on the suggested inputs for this testing file from the clients?

[BollepalliPranitha]

@adhampton110 Can you test for these sequences .
AYGU-1_MeltR.csv
BLYA-1.1_MeltR.csv
IH-1_MeltR-260.csv

AYGU-1_MeltR.csv
Sample 1
No Blanks
Wavelength – 260
Nucleic acid type – RNA
Sequence – GACUAGUU
Molecular state - Homoduplex

Sample 2
BLYA-1.1_MeltR.csv
No Blanks
Wavelength – 260
Nucleic acid type – RNA
Sequence – CCACGUCUCG,CGAGAGUGG
Molecular state - Heteroduplex

Sample 3
IH-1_MeltR-260.csv
No Blanks
Wavelength – 260
Nucleic acid type – RNA
Sequence - GGCGUIAUAGCC
Molecular state - Monomolecular

I have provided data for monomolecular, heteroduplex, and homoduplex samples.
The format of the data is similar in all the three files
So we need to test against these values

[adhampton110]

@BollepalliPranitha

I had successful uploads with Sample 1 & Sample 2. I ran into this error message using Sample 3. Taking a look at the MeltR source code, I am hitting this error.

I am wondering if we are to specify the coefficients, as opposed to specifying the sequence

[BollepalliPranitha]

@adhampton110
could you please send me all the values you used for this format of data
I think the sequence specified is an issue.
Will update you regarding the sequence.

[adhampton110]

@BollepalliPranitha

Here are the raw inputs I am passing directly into the meltR.A function. masterFrame is the IH-1_MeltR-260.csv file, as a data frame object:

[BollepalliPranitha]

@adhampton110 Have you tried using any other sequence for Monomolecular
because I cant find the "I" included in the code

Try for other sequences
I don't think Monomolecular option is working for any sequences .

[adhampton110]

@BollepalliPranitha I have not, which is why I have been attempting to interact with the MeltR package directly within the R console. With the specified inputs you gave me, if we aren't able to create a meltR.A object when directly interacting with the package, then we also are not going to be able to create a meltR.A object with our application code. Our app code just calls the meltR.A function.

[BollepalliPranitha]

@adhampton110
for sample 3 , can you try with sequence "GGCGUGAUAGCC"
This is suggested by client

[adhampton110]

@BollepalliPranitha I am unable to reproduce their successful creation. Have you attempted to create the meltR.A object with the inputs from the screenshot?

The screenshot contains a syntax error, around the fitTs parameter, to which I believe the value would be set to NULL but the methods parameter would be set to c(TRUE, TRUE, TRUE). Is this the full screenshot?

[adhampton110]

This is exactly what I am inputting into the meltR.A function. Please let me know if my inputs are incorrect.

[BollepalliPranitha]

@adhampton110 I think there are so many outliers present in the data provided that should be manually handled. I am in discussing this with client. The issue persists with the data and Sequence.

[BollepalliPranitha]

This issue is related to the newly created issue #185