iswitch

Installation

not yet published

to install it locally, clone it from github:

git clone https://github.com/strasserle/iswitch

change into the outer folder 'iswitch' and install the package:

cd iswitch
pip install .

Run example data

Download the following data into the data directory:

• pheno
• Data_tsv and annotation_file

In python, use the following line to try the example data:

from iswitch import isoform_switch_analyzer as isa
switches, switch_pair_df = isa.detect_iswitches()

The last line is equivalent to:

switches, switch_pair_df = sa.detect_iswitches(method="isa",
                 pheno="iswitch\\data\\TCGA_phenotype_denseDataOnlyDownload.tsv.gz",
                 data="iswitch\\data\\tcga_Kallisto_tpm.gz",
                 disease="iswitch\\kidney-clear-cell-carcinoma",
                 anno="iswitch\\data\\gencode.v23.annotation.transcript.probemap")

Input format

To detect isoform switches in custom data, specify the following params as follows:

• pheno: Tab separated gz file with a column "sample" and the according phenotype in a column called "primary_disease" as well as a column "sample_type_id" where a 1 denotes case samples and a 11 control samples. Note that this notation is inferred from TCGA.
• data: Tab separated table where the columns represent the samples (same sample ids as in pheno) and the rows represent the isoforms (same ids as in annotation_file).
• disease: The primary disease you are interested in.
• anno: Tab separated file with the columns "id" and "gene" which give the gene id for each transcript.

Options

• The default method is "isa", which is a python version of the R package IsoformSwitchAnalyzer.

• Alternatively, if the package SPADA can be used. After pip install spada, use:

  isa.detect_iswitches(method="spada")

Visualize output

To visualize all isoform switches detected for a certain gene, try:

example_plot_switches(gene_id, switch_pair_df, switches, casecolor, controlcolor) # or 
example_plot_switches_reordered(gene_id, switch_pair_df, switches, casecolor, controlcolor)

To do an enrichment analysis, install the CORUM core complexes file into the data directory and run:

prot_complex_table, prot_complex_dict = enrichment(switch_pairs)

To draw a graph of a certain protein complex, use afterwards:

draw_protein_graph(complex_name, switch_df, prot_complex_table, prot_complex_dict)

Climente-González, H., Porta-Pardo, E., Godzik, A., and Eyras, E. (2017). The Functional Impact of Alternative Splicing in Cancer. Cell Reports 20, 2215–2226.