lm22 is a gene expression signature matrix used in the EPIC and IOBR
packages for estimating the proportions of different immune cell types from
bulk RNA-seq data. It contains reference profiles for multiple immune cell
types,
including various B cell and T cell subsets, as well as plasma cells and
other immune cell types.
Usage
data(lm22)Format
A list of length 2:
refProfilesA numeric matrix where rows represent genes and columns represent different immune cell types. The matrix provides gene expression profiles used as references for deconvolution in the EPIC model. The number of columns may vary depending on the number of immune cell types included in the reference profiles.
cellTypesA character vector containing the names of the immune cell types included in the reference profiles.
Examples
data(lm22)
head(lm22)
#> B cells naive B cells memory Plasma cells T cells CD8 T cells CD4 naive
#> ABCB4 555.71345 10.74423 7.225819 4.31128 4.60586
#> ABCB9 15.60354 22.09479 653.392328 24.22372 35.67151
#> ACAP1 215.30595 321.62102 38.616872 1055.61338 1790.09717
#> ACHE 15.11795 16.64885 22.123737 13.42829 27.18773
#> ACP5 605.89738 1935.20148 1120.104684 306.31252 744.65660
#> ADAM28 1943.74270 1148.12014 324.780800 22.68972 40.06171
#> T cells CD4 memory resting T cells CD4 memory activated
#> ABCB4 7.406442 8.043976
#> ABCB9 30.048192 38.455423
#> ACAP1 922.152747 340.883424
#> ACHE 18.444927 13.441268
#> ACP5 557.819820 248.546932
#> ADAM28 21.233311 15.209620
#> T cells follicular helper T cells regulatory (Tregs) T cells gamma delta
#> ABCB4 6.469993 7.833082 9.312295
#> ABCB9 17.604795 46.073657 19.715722
#> ACAP1 1107.798265 1995.482601 280.075719
#> ACHE 14.805542 24.652712 33.658448
#> ACP5 711.949744 958.916018 493.969120
#> ADAM28 24.281406 74.766335 24.370752
#> NK cells resting NK cells activated Monocytes Macrophages M0
#> ABCB4 13.68284 4.556713 6.202496 7.95136
#> ABCB9 21.86372 16.396143 20.309426 56.25189
#> ACAP1 512.63691 387.581742 190.879024 48.97222
#> ACHE 16.65374 13.441268 16.375268 13.69296
#> ACP5 340.82014 239.277068 512.931382 13644.17230
#> ADAM28 193.60939 94.405818 58.311203 54.96649
#> Macrophages M1 Macrophages M2 Dendritic cells resting
#> ABCB4 27.55771 121.43228 114.63675
#> ABCB9 29.38088 40.39026 123.99331
#> ACAP1 30.97425 23.05515 61.38655
#> ACHE 1373.06962 48.58576 16.71547
#> ACP5 1062.47591 7633.96018 13825.05363
#> ADAM28 274.64000 360.68204 37.29173
#> Dendritic cells activated Mast cells resting Mast cells activated
#> ABCB4 4.872184 4.727985 34.11366
#> ABCB9 23.384603 53.466757 23.61575
#> ACAP1 26.412923 104.200198 73.60793
#> ACHE 193.159977 13.948778 20.50125
#> ACP5 3989.865169 263.497930 323.38128
#> ADAM28 53.219649 137.853628 116.87950
#> Eosinophils Neutrophils
#> ABCB4 15.03053 14.90689
#> ABCB9 29.78644 33.67915
#> ACAP1 696.44280 596.02596
#> ACHE 40.41493 22.76649
#> ACP5 860.56337 307.14280
#> ADAM28 546.00616 128.68607