DisHet: Heterogeneity Dissection
In DisHet: Estimate the Gene Expression Levels and Component Proportions of the Normal, Stroma (Immune) and Tumor Components of Bulk Tumor Samples
Description
Usage
Arguments
Details
Examples
Description
This function performs dissection of bulk sample gene expression using matched normal and tumorgraft RNA-seq data. It outputs the final proportion estiamtes of the three components for all patients.
The patient-specific dissection proportion estimates are saved in a 3-by-k matrix named "rho", where k is the number of patients. The 3 rows of "rho" matrix correspond to the tumor, normal, stroma components in order. That is, the proportion estimate of tumor component for patient i is stored in rho[1,i]; the normal component proportion estimate of this patient is stored in rho[2,i];and stroma component proportion in rho[3,i].
Usage
1
2
3
Arguments
exp_T
Gene expression in bulk RNA-seq samples. The rows correspond to different genes. The columns correspond to different patients.
exp_N
Gene expression in the corresponding normal samples. The rows list the same set of genes as in exp_G. The columns correspond to patients matched with exp_T.
exp_G
Gene expression in the corresponding tumor samples. The rows list the same set of genes as in exp_G. The columns correspond to patients matched with exp_T.
save
When save==TRUE, as in default, all component proportion estimates during MCMC iterations can be saved into a user-specified directory using the "MCMC_folder" argument.
MCMC_folder
Directory for saving the estimated mixture proportion matrix updates during MCMC iterations. The default setting is to create a "DisHet" folder under the current working directory.
n_cycle
Number of MCMC iterations(chain length). The default value is 10,000.
save_last
Save the rho matrix updates for the last "save_last" Number of MCMC iterations. The default value is 500.
mean_last
Calculate the final proportion estiamte matrix using the last "mean_last" number of MCMC iterations. The default value is 200.
dirichlet_c
Stride scale in sampling rho. Larger value leads to smaller steps in sampling rho. The default value is 1.
S_c
Stride scale in sampling Sij. Larger value leads to larger steps in sampling Sij. The default value is 1.
rho_small
The smallest rho updates allowed during MCMC. The default is 1e-2. This threshold is set to help improve numerical stability of the algorithm.
initial_rho_S
Initial value of the proportion estimate for the stroma component. The default value is 0.02.
initial_rho_G
Initial value of the proportion estimate for the tumor component. The default value is 0.96.
initial_rho_N
Initial value of the proportion estimate for the normal component. The default value is 0.02.
Details
Un-logged expression values should be used in exp_N/T/G matrices, and their rows and columns must match each other corresponding to the same set of genes and patients.
The values specified for "initial_rho_S", "initial_rho_G", and "initial_rho_S" all have to be positive. If the three proportion initials are not summing to 1, normalization is performed automatically to force the sum to be 1.
Examples
1
2
3
4
5
6
load(system.file("example/example_data.RData",package="DisHet"))
exp_T <- exp_T[1:200,]
exp_N <- exp_N[1:200,]
exp_G <- exp_G[1:200,]
rho <- DisHet(exp_T, exp_N, exp_G, save=FALSE, n_cycle=200, mean_last=50)
Example output
Loading required package: gtools
Loading required package: matrixStats
Overall acceptance rate for S: 0.65
Overall acceptance rate for rho: 0.13
Finished iteration 1
Overall acceptance rate for S: 0.77
Overall acceptance rate for rho: 0.13
Finished iteration 2
Overall acceptance rate for S: 0.76
Overall acceptance rate for rho: 0.13
Finished iteration 3
Overall acceptance rate for S: 0.72
Overall acceptance rate for rho: 0.15
Finished iteration 4
Overall acceptance rate for S: 0.73
Overall acceptance rate for rho: 0.17
Finished iteration 5
Overall acceptance rate for S: 0.69
Overall acceptance rate for rho: 0.17
Finished iteration 6
Overall acceptance rate for S: 0.7
Overall acceptance rate for rho: 0.17
Finished iteration 7
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 8
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.09
Finished iteration 9
Overall acceptance rate for S: 0.66
Overall acceptance rate for rho: 0.09
Finished iteration 10
Overall acceptance rate for S: 0.67
Overall acceptance rate for rho: 0.14
Finished iteration 11
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.09
Finished iteration 12
Overall acceptance rate for S: 0.68
Overall acceptance rate for rho: 0.09
Finished iteration 13
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.13
Finished iteration 14
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.13
Finished iteration 15
Overall acceptance rate for S: 0.65
Overall acceptance rate for rho: 0.09
Finished iteration 16
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.09
Finished iteration 17
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.13
Finished iteration 18
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.09
Finished iteration 19
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.09
Finished iteration 20
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.04
Finished iteration 21
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.09
Finished iteration 22
Overall acceptance rate for S: 0.64
Overall acceptance rate for rho: 0.15
Finished iteration 23
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.04
Finished iteration 24
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.09
Finished iteration 25
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.13
Finished iteration 26
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 27
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.09
Finished iteration 28
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 29
Overall acceptance rate for S: 0.56
Overall acceptance rate for rho: 0.09
Finished iteration 30
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.13
Finished iteration 31
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.09
Finished iteration 32
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.14
Finished iteration 33
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.09
Finished iteration 34
Overall acceptance rate for S: 0.66
Overall acceptance rate for rho: 0.14
Finished iteration 35
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.14
Finished iteration 36
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.13
Finished iteration 37
Overall acceptance rate for S: 0.56
Overall acceptance rate for rho: 0.13
Finished iteration 38
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 39
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 40
Overall acceptance rate for S: 0.64
Overall acceptance rate for rho: 0.09
Finished iteration 41
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.13
Finished iteration 42
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.18
Finished iteration 43
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 44
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.1
Finished iteration 45
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.11
Finished iteration 46
Overall acceptance rate for S: 0.64
Overall acceptance rate for rho: 0.13
Finished iteration 47
Overall acceptance rate for S: 0.65
Overall acceptance rate for rho: 0.13
Finished iteration 48
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 49
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.13
Finished iteration 50
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 51
Overall acceptance rate for S: 0.54
Overall acceptance rate for rho: 0.17
Finished iteration 52
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.09
Finished iteration 53
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 54
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.13
Finished iteration 55
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.17
Finished iteration 56
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.22
Finished iteration 57
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.21
Finished iteration 58
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.22
Finished iteration 59
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.22
Finished iteration 60
Overall acceptance rate for S: 0.56
Overall acceptance rate for rho: 0.21
Finished iteration 61
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.21
Finished iteration 62
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.3
Finished iteration 63
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.23
Finished iteration 64
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.18
Finished iteration 65
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.18
Finished iteration 66
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.23
Finished iteration 67
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.15
Finished iteration 68
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.14
Finished iteration 69
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.18
Finished iteration 70
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.09
Finished iteration 71
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.14
Finished iteration 72
Overall acceptance rate for S: 0.55
Overall acceptance rate for rho: 0.15
Finished iteration 73
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 74
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.14
Finished iteration 75
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.18
Finished iteration 76
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.14
Finished iteration 77
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.15
Finished iteration 78
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.14
Finished iteration 79
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.14
Finished iteration 80
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.07
Finished iteration 81
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.13
Finished iteration 82
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 83
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.17
Finished iteration 84
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.17
Finished iteration 85
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 86
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 87
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 88
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 89
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 90
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.25
Finished iteration 91
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 92
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.16
Finished iteration 93
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 94
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.14
Finished iteration 95
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.22
Finished iteration 96
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.09
Finished iteration 97
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.18
Finished iteration 98
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.18
Finished iteration 99
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.22
Finished iteration 100
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.13
Finished iteration 101
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 102
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.17
Finished iteration 103
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 104
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 105
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.17
Finished iteration 106
Overall acceptance rate for S: 0.55
Overall acceptance rate for rho: 0.09
Finished iteration 107
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 108
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 109
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 110
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.13
Finished iteration 111
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.17
Finished iteration 112
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 113
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 114
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 115
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 116
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.18
Finished iteration 117
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.13
Finished iteration 118
Overall acceptance rate for S: 0.64
Overall acceptance rate for rho: 0.17
Finished iteration 119
Overall acceptance rate for S: 0.54
Overall acceptance rate for rho: 0.17
Finished iteration 120
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.09
Finished iteration 121
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.13
Finished iteration 122
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.18
Finished iteration 123
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.09
Finished iteration 124
Overall acceptance rate for S: 0.56
Overall acceptance rate for rho: 0.11
Finished iteration 125
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.09
Finished iteration 126
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 127
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 128
Overall acceptance rate for S: 0.55
Overall acceptance rate for rho: 0.16
Finished iteration 129
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 130
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.22
Finished iteration 131
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.13
Finished iteration 132
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.09
Finished iteration 133
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 134
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.13
Finished iteration 135
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 136
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 137
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.12
Finished iteration 138
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 139
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 140
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.22
Finished iteration 141
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.22
Finished iteration 142
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 143
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.13
Finished iteration 144
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.13
Finished iteration 145
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 146
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 147
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 148
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 149
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 150
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 151
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 152
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.17
Finished iteration 153
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.13
Finished iteration 154
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.13
Finished iteration 155
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.17
Finished iteration 156
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 157
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 158
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 159
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.2
Finished iteration 160
Overall acceptance rate for S: 0.65
Overall acceptance rate for rho: 0.13
Finished iteration 161
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 162
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.13
Finished iteration 163
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 164
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 165
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 166
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 167
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 168
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 169
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 170
Overall acceptance rate for S: 0.56
Overall acceptance rate for rho: 0.17
Finished iteration 171
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.17
Finished iteration 172
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.09
Finished iteration 173
Overall acceptance rate for S: 0.56
Overall acceptance rate for rho: 0.17
Finished iteration 174
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 175
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.17
Finished iteration 176
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.17
Finished iteration 177
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 178
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.13
Finished iteration 179
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 180
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 181
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.17
Finished iteration 182
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 183
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 184
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.13
Finished iteration 185
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 186
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.17
Finished iteration 187
Overall acceptance rate for S: 0.64
Overall acceptance rate for rho: 0.17
Finished iteration 188
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 189
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.13
Finished iteration 190
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.11
Finished iteration 191
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 192
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 193
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 194
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.16
Finished iteration 195
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.08
Finished iteration 196
Overall acceptance rate for S: 0.55
Overall acceptance rate for rho: 0.18
Finished iteration 197
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.17
Finished iteration 198
Overall acceptance rate for S: 0.57
Overall acceptance rate for rho: 0.17
Finished iteration 199
Overall acceptance rate for S: 0.6
Overall acceptance rate for rho: 0.17
Finished iteration 200
DisHet documentation built on May 2, 2019, 2:42 a.m.
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Description Usage Arguments Details Examples
Description
This function performs dissection of bulk sample gene expression using matched normal and tumorgraft RNA-seq data. It outputs the final proportion estiamtes of the three components for all patients.
The patient-specific dissection proportion estimates are saved in a 3-by-k matrix named "rho", where k is the number of patients. The 3 rows of "rho" matrix correspond to the tumor, normal, stroma components in order. That is, the proportion estimate of tumor component for patient i is stored in rho[1,i]; the normal component proportion estimate of this patient is stored in rho[2,i];and stroma component proportion in rho[3,i].
Usage
1 2 3 |
Arguments
exp_T |
Gene expression in bulk RNA-seq samples. The rows correspond to different genes. The columns correspond to different patients. |
exp_N |
Gene expression in the corresponding normal samples. The rows list the same set of genes as in exp_G. The columns correspond to patients matched with exp_T. |
exp_G |
Gene expression in the corresponding tumor samples. The rows list the same set of genes as in exp_G. The columns correspond to patients matched with exp_T. |
save |
When save==TRUE, as in default, all component proportion estimates during MCMC iterations can be saved into a user-specified directory using the "MCMC_folder" argument. |
MCMC_folder |
Directory for saving the estimated mixture proportion matrix updates during MCMC iterations. The default setting is to create a "DisHet" folder under the current working directory. |
n_cycle |
Number of MCMC iterations(chain length). The default value is 10,000. |
save_last |
Save the rho matrix updates for the last "save_last" Number of MCMC iterations. The default value is 500. |
mean_last |
Calculate the final proportion estiamte matrix using the last "mean_last" number of MCMC iterations. The default value is 200. |
dirichlet_c |
Stride scale in sampling rho. Larger value leads to smaller steps in sampling rho. The default value is 1. |
S_c |
Stride scale in sampling Sij. Larger value leads to larger steps in sampling Sij. The default value is 1. |
rho_small |
The smallest rho updates allowed during MCMC. The default is 1e-2. This threshold is set to help improve numerical stability of the algorithm. |
initial_rho_S |
Initial value of the proportion estimate for the stroma component. The default value is 0.02. |
initial_rho_G |
Initial value of the proportion estimate for the tumor component. The default value is 0.96. |
initial_rho_N |
Initial value of the proportion estimate for the normal component. The default value is 0.02. |
Details
Un-logged expression values should be used in exp_N/T/G matrices, and their rows and columns must match each other corresponding to the same set of genes and patients.
The values specified for "initial_rho_S", "initial_rho_G", and "initial_rho_S" all have to be positive. If the three proportion initials are not summing to 1, normalization is performed automatically to force the sum to be 1.
Examples
1 2 3 4 5 6 | load(system.file("example/example_data.RData",package="DisHet"))
exp_T <- exp_T[1:200,]
exp_N <- exp_N[1:200,]
exp_G <- exp_G[1:200,]
rho <- DisHet(exp_T, exp_N, exp_G, save=FALSE, n_cycle=200, mean_last=50)
|
Example output
Loading required package: gtools
Loading required package: matrixStats
Overall acceptance rate for S: 0.65
Overall acceptance rate for rho: 0.13
Finished iteration 1
Overall acceptance rate for S: 0.77
Overall acceptance rate for rho: 0.13
Finished iteration 2
Overall acceptance rate for S: 0.76
Overall acceptance rate for rho: 0.13
Finished iteration 3
Overall acceptance rate for S: 0.72
Overall acceptance rate for rho: 0.15
Finished iteration 4
Overall acceptance rate for S: 0.73
Overall acceptance rate for rho: 0.17
Finished iteration 5
Overall acceptance rate for S: 0.69
Overall acceptance rate for rho: 0.17
Finished iteration 6
Overall acceptance rate for S: 0.7
Overall acceptance rate for rho: 0.17
Finished iteration 7
Overall acceptance rate for S: 0.61
Overall acceptance rate for rho: 0.13
Finished iteration 8
Overall acceptance rate for S: 0.63
Overall acceptance rate for rho: 0.09
Finished iteration 9
Overall acceptance rate for S: 0.66
Overall acceptance rate for rho: 0.09
Finished iteration 10
Overall acceptance rate for S: 0.67
Overall acceptance rate for rho: 0.14
Finished iteration 11
Overall acceptance rate for S: 0.58
Overall acceptance rate for rho: 0.09
Finished iteration 12
Overall acceptance rate for S: 0.68
Overall acceptance rate for rho: 0.09
Finished iteration 13
Overall acceptance rate for S: 0.59
Overall acceptance rate for rho: 0.13
Finished iteration 14
Overall acceptance rate for S: 0.62
Overall acceptance rate for rho: 0.13
Finished iteration 15
Overall acceptance rate for S: 0.65
Overall acceptance rate for rho: 0.09
Finished iteration 16
Overall acceptance rate for S: 0.6
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