View source: R/GEX_pseudobulk.R
GEX_pseudobulk | R Documentation |
Function that performs pseudo-bulking on the data (VGM input), according to criteria specified by the User, and uses the pseudo-bulked data to perform Differential Gene Expression (DGE) analysis.
GEX_pseudobulk( vgm.input, column.group, group1, group2, column.comparison, comparison, pool, platypus.version )
vgm.input |
Output of the VDJ_GEX_matrix function. Mandatory |
column.group |
Character vector. Mandatory. Column name of VDJ_GEX_matrix[[2]] where the groups to be tested for differenetial gene expression are located |
group1 |
Strings vector. Mandatory. Samples to be grouped together for differential expression analysis against group2 (if pool=TRUE or column.comparison!=NULL). If pool=FALSE, vector containing samples to be tested individually against samples with the same index in the vector of group2. |
group2 |
Strings vector. Mandatory. Samples to be grouped together for differential expression analysis against group1 (if pool=TRUE or column.comparison!=NULL). If pool=FALSE, vector containing samples to be tested individually against samples with the same index in the vector of group1. |
column.comparison |
Character vector. Defaults to NULL. Column name of VDJ_GEX_matrix[[2]] where the comparison cathegories are located, if DGE between group1 and group2 is performed across diferrent cathegories. |
comparison, |
Strings vector. Defaults to NULL. Comparison cathegories, if more than one is present. |
pool |
Logical. Defaults to FALSE. Indicates whether samples specified in group1 and group2 are to be pooled together within the same group. |
platypus.version |
This function works with "v3" only, there is no need to set this parameter |
A data.frame or list of data.frames containing the results of the DGE analysis for every level of pseudo-bulking.
## Not run: pseudo_DE<-GEX_pseudobulk( vgm.input=VGM_NP396_GP33_GP66_labelled, column.group="sample_id", group1 = c("s1"), group2 = c("s4"), column.comparison = "seurat_clusters", comparison=c(2,3,5,9), pool=FALSE) ## End(Not run)
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