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atac_geo_processed_matrices_neurons_T.R
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atac_geo_processed_matrices_neurons_T.R
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###neurons
#separately get the KS1 and KS2 matrices
mat <- peaks_by_samples[, -which(colnames(peaks_by_samples) == "Cohort9_2-22_wt")]
sampinf <- sample_info[-which(colnames(peaks_by_samples) == "Cohort9_2-22_wt"), ]
dds <- getDDSObject(mat, sampinf, "KS1", "9")
dds2 <- getDDSObject(peaks_by_samples, sample_info, "KS2", c("1", "8"))
mat1 <- mat[, which(sampinf$genotype %in% c("WT", "KS1") &
sampinf$cohort %in% c("9"))]
mat2 <- peaks_by_samples[, which(sample_info$genotype %in% c("WT", "KS2") &
sample_info$cohort %in% c("1", "8"))]
#combine the KS1 and KS2 matrices
geo_mat_neurons <- cbind(mat1, mat2)
geo_mat_neurons_df <- as.data.frame(geo_mat_neurons)
library(tibble)
geo_mat_neurons_df <- rownames_to_column(geo_mat_neurons_df, "mm10_coordinates")
write_csv(geo_mat_neurons_df, "GEO/neurons_paper_2023/atac_peaks_by_samples_matrix_neurons.csv")
###T cells
#get the KS1 and KS2 matrices combined
geo_mat_T <- peaks_by_samples[, grep("_T_", colnames(peaks_by_samples))]
geo_mat_T_df <- as.data.frame(geo_mat_T)
geo_mat_T_df <- rownames_to_column(geo_mat_T_df, "mm10_coordinates")
write_csv(geo_mat_T_df, "GEO/neurons_paper_2023/atac_peaks_by_samples_matrix_T.csv")
###neurons (KS1 replication samples)
mat <- peaks_by_samples[, -which(colnames(peaks_by_samples) == "Cohort8-12_KS1")]
sampinf <- sample_info[-which(colnames(peaks_by_samples) == "Cohort8-12_KS1"), ]
mat3 <- mat[, which(sampinf$genotype %in% c("KS1") &
sampinf$cohort %in% c("8"))]
geo_mat_neurons_replication <- mat3
geo_mat_neurons_replication_df <- as.data.frame(geo_mat_neurons_replication)
library(tibble)
geo_mat_neurons_replication_df <- rownames_to_column(geo_mat_neurons_replication_df, "mm10_coordinates")
write_csv(geo_mat_neurons_replication_df, "GEO/neurons_paper_2023/atac_peaks_by_samples_matrix_neurons_replication.csv")
###T cells RNA-seq
#get combined_mat as in the "diff_expr_analysis_B_and_T_Dec2023.R"
expr_mat_df <- as.data.frame(combined_mat[, grep("_T_", colnames(combined_mat))])
geo_mat_T_cells_df <- rownames_to_column(expr_mat_df, "Ensembl_ID")
write_csv(geo_mat_T_cells_df, "GEO/neurons_paper_2023/rna_genes_by_samples_matrix_T_cells.csv")