Kstar Ess

[Dot Liljenquist]

Givennetwork files declared in globals, create pickles of the kstar object that can then be quickly loaded in analysisAssumes that the Network structure has two folders Y and ST under the NETWORK_DIR global variable and that all .csv files in those directories should be loaded into a network pickle.

Pandas dataframe of an experiment that has a reference accession, a peptide column and/or a site column. The peptide column should be upper case, with lower case indicating the site of phosphorylation - this is preferredThe site column should be in the format S/T/Y, e.g. Y15 or S345

Map the peptide/sites to the common sequence reference and remove and report errors for sites that do not align as expected.expMapper.align_sites(window=7). Operates on the experiment dataframe of class.

Kinase Activity calculates the estimated activity of kinases given an experiment using hypergeometric distribution.Hypergeometric distribution examines the number of protein sites found to be active in evidence compared to the number of protein sites attributed to a kinase on a provided network.

For a kinact_dict, where random generation and activity has already been run for the phospho_types of interest, this will calculate the Mann-Whitney U test for comparing the array of p-values for real data to those of random data, across the number of networks used.

Calculates combined activity of experiments based that uses a threshold value to determine if an experiment sees a site or not To use values use 'mean' as agg mean aggregation drops NA values from consideration To use count use 'count' as agg - present if not na

For a kinact_dict, where random generation and activity has already been run for the phospho_types of interest, this will calculate the Mann-Whitney U test for comparing the array of p-values for real data to those of random data, across the number of networks used.It will also calculate the false positive rate for a pvalue, given observations of a random bootstrapping analysis

The DotPlot class is used for plotting dotplots, with the option to add clustering and context plots.The size of the dots based on the values dataframe, where the size of the dot is the area of the value * dotsize

The distance metric to use in the case that y is a collection of observation vectors; ignored otherwise. See the pdist function for a list of valid distance metrics. A custom distance function can also be used.

Function to establish a kstar KinaseActivity object from an experiment with an activity logadd the networks, calculate, aggregate, and summarize the hypergeometric enrichment into a final activity object. Should be followed by randomized_analyis, then Mann_Whitney_analysis.

Creates random experiments, drawn from the human phosphoproteome, according to the distribution of the number of compendiathat each data column in the experiment has for num_random_experiments. Kinase activity calculation is then run on every random experiment.

Given the name and output directory of a saved kstar analyis from the nextflow pipeline, load the results into new kinact object withthe minimum dataframes required for analysis (binary experiment, hypergeometric activities, normalized activities, mann whitney activities)

Given the name and output directory of a saved kstar analyis, load the parameters and minimum dataframes needed for reinstantiating a kinact objectThis minimum list will allow you to repeat normalization or mann whitney at a different false positive rate threshold and plot results.

Having performed kinase activities (run_kstar_analyis), save each of the important dataframes to files and the final pickleSaves an activities, aggregated_activities, summarized_activities tab-separated filesSaves a pickle file of dictionary

Having performed kinase activities (run_kstar_analyis), save each of the important dataframes, minimizing the memory storage needed to get back to a rebuilt version for plotting results and analysis. For each phospho_type in the kinact_dict, this will save three .tsv files for every activitiesanalysis run, two additional if random analysis was run, and two more if Mann Whitney based analysis was run. It also creates a readme file of the parameter values used

Below are some FAQ's, that may help you.

Junior or Open class?

Just a reminder that classes labelled 'OPEN' is for all ages as we do not restrict age against talent. KSTAR encourages higher level of learning if one is 1. Wanting the challenge 2. Ready to go to next stage.

These specific age categories are used because of dance competition or project requriements.

How do i choose class/es?

Please email kstarstud...@gmail.com or direct message us on instagram. Include, age and experience.

I want to register, right away.

Not a problem, please refer to: -pro.com/online/kstarstudios

I have already registered, what do i do next?

Easy! Please go to your account and select your classes that you choose to ENROL in for Trimester 1, 2022. Check if all your static details are correct.

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