Function to prepare the input for `cluster_communication()` by using DEG analysis results data
preparing_DEG_list.RdThe function prepares the input for `cluster_communication()` analysis by using DEG results data
Arguments
- cluster
column of the result table of DEG analysis with the data of the clusters under analysis
- p_val
column of the result table of DEG analysis with the data of the p-value of the test. Could be either nominal or adjusted p-value
- log2FC
column of the result table of DEG analysis with the data of the log2Fold Change
- gene
column of the result table of DEG analysis with the names of the genes tested
- universe
vector with the names of the genes of interest in the study. This value should be the names in the LR network
Value
The function returns a gene list composed by a vector for each cluster provided. Each vector is composed by the score, calculated as abs(log2FC) * -log10(p-value), named by the respective genes
Details
The function prepares the gene list in a format compatible with the `cluster_communication()` analysis. In detail, the function needs some information obtained from DEG analysis: cluster tested, gene names, p-values, log2(Fold Change). These data will be filtered to consider only the gene of interest in the study (`universe`). The function calculates a score for each gene as: abs(log2FC) * -log10(p-value). If the p-value is 0, this is approximated to 1/10 of the minimum non-zero p-value present in the data. The function returns a gene set list for each cluster, each composed by a vector of scores named after the genes names provided.