add_pathways | R Documentation |
Please note that only sample_id column
, and columns with .Amp, .Del, .fus or no suffix are accepted.
Any gene column with no suffix will be assumed to be a mutation.
add_pathways(
gene_binary,
pathways = c(names(gnomeR::pathways)),
custom_pathways = NULL,
other_vars = NULL,
count_pathways_by = deprecated()
)
gene_binary |
a binary matrix from |
pathways |
a vector of pre-coded pathways to annotate. The options are |
custom_pathways |
a vector of alterations to annotate as a single pathway, or a list of custom pathways (see |
other_vars |
One or more column names (quoted or unquoted) in data to be retained in resulting data frame. Default is NULL. |
count_pathways_by |
deprecated |
Input a binary matrix of patients x alterations and return a dataframe with a column per pathway indicating if default or custom oncogenic signaling pathways are activated in each sample. Default package pathways were sourced from Sanchez-Vega, F et al., 2018.
Please check for gene aliases in your data set before using.
a data frame: each sample is a row, columns are pathways, with values of 0/1 depending on pathway alteration status.
Sanchez-Vega, F., Mina, M., Armenia, J., Chatila, W. K., Luna, A., La, K. C., Dimitriadoy, S., Liu, D. L., Kantheti, H. S., Saghafinia, S., Chakravarty, D., Daian, F., Gao, Q., Bailey, M. H., Liang, W. W., Foltz, S. M., Shmulevich, I., Ding, L., Heins, Z., Ochoa, A., … Schultz, N. (2018). Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell, 173(2), 321–337.e10. https://doi.org/10.1016/j.cell.2018.03.035
gene_binary <- create_gene_binary(mutation = gnomeR::mutations,
cna = gnomeR::cna,
fusion = gnomeR::sv)
pathway_df <- add_pathways(gene_binary, pathways = "Notch")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.