getHTTrDEG: Gets the effect of each chemical treatment on probes
In i-shah/httRws: Obtain HTTr data from NCCT webservices

Description Usage Arguments Details Value Examples

This function returns the results from DESeq2 analysis of the raw count data by using the replicates for each sample across multiple plates as well as the DMSO conrols for each treatment group (conc). Just calling this with the sid wil return a long skinny format df. The skinny df has all the information for filtering the results. Optionally, these results can be filtered by p-values, minimum average count l2fc magnitude and also pivoted to create wide df (more suitable for analysis)

1 2	getHTTrDEG(sid, mncnt0 = NULL, p0 = NULL, l2fc0 = NULL, pivot_on = NULL, pivot_func = NULL)

`sid`	A valid dsstox_sid (e.g. from searchHTTrChem)
`p0`	the the unadjusted p-value cut-off for each probe (optional)
`l2fc0`	the min abs(L2FC) threshold (optional)
`pivot_on`	whether to pivot and how. Values NULL: no pivot provide skinny results gene: pivot on gene symbol probe_id: pivot on probe_id
`mincnt0`	the min average raw count of the probe across reps (optional)
`pivot_func:`	if pivot_on=='gene' then how to aggregate l2fc max: take the max +ve or min -ve mean: take the average

Note: a) If the chemical was run mulitple times then there will be multiple sample ids! b) If filters are used to exclude probes by any criterion then the missing value is replaced with 0.0 (naught) c) Keep the skinny format without pivoting if you want to see all the data

a named list with two dataframes l2fc: all L2FC data by probe_id/genen (columns) x treatment groups (rows) index: the index columns in the L2FC dataframe

    X <- getHTTrDEG('DTXSID7020182')
    X <- getHTTrDEG('DTXSID7020182',mncnt0=100)
    X <- getHTTrDEG('DTXSID7020182',mncnt0=100,p0=0.05)
    X <- getHTTrDEG('DTXSID7020182',mncnt0=100,p0=0.05,l2fc0=2)
    X <- getHTTrDEG('DTXSID7020182',mncnt0=100,p0=0.1,l2fc0=0.6,pivot_on='gene', pivot_func='max')