KM analysis: Filtering to One Sample Per Patient
Have you ever noticed this icon in the top corner of a KM plot?
This means that some patients have more than one sample in the plot. This can happen when a patient has both a tumor and normal sample or when a patient has a metastasis that is part of the dataset.
To filter down to one sample per patient, start with your column of data that you wish to perform a KM analysis on. For this example we're going to use IDH1 mutation status in TCGA Lower Grade Glioma.
- To start, make sure that one of your variables is IDH1 mutation and that your other is the Phenotype column of 'sample type'. Note that different datasets may call this phenotype data something slightly different. We are just trying to add a column of data that indicates the sample type such as 'Primary Tumor', 'Normal', etc.
We can see here that some patients have both Primary and Recurrent Tumors. To filter out the samples that are 'Recurrent Tumor', type 'primary' into the filter search box.
- Next, click the filter icon next to the filter search box and chose 'Filter'. This will filter out all samples that are not primary tumor.
- Voila! Run your KM analysis by clicking the caret menu at the top of the column and choosing 'Kaplan-Meier plot' It will now only have primary tumor samples in it!