-
Notifications
You must be signed in to change notification settings - Fork 6
/
ResSummary2.r
549 lines (457 loc) · 21.7 KB
/
ResSummary2.r
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
# sample R script file
# used to determine the summary statistics of various ChIP seq samples
# within a particular experiment (run)
# author: Sourya Bhattacharyya
# Vijay-AY lab
#==============
# Execution command:
# Rscript ResSummary2.r $OutBaseDir $BAMRead $Tagmentation $OldMethod
# input arguments:
# 1) OutBaseDir: Directory under which results of all the different samples are stored
# 2) BAMRead: Boolean variable, indicating if the BAM files were used for analysis (1) or fastq (0). Default 0
# 3) Tagmentation: Binary variable. If 1, denotes that the data samples have been under ChIPMentation method. Default 0.
# 4) OldMethod: Binary variable. If 1, old summary statistics is used for performance evaluation. Default 0 (preferred).
# 5) ControlPeak: Variable with value of either 0, 1 or 2. If 1, control samples has been used for peak calling.
# If 0, no control sample is used. If 2, peaks using control and not using control both exist. Default 0.
# sample execution command:
# Rscript ResSummary2.r /home/sourya/ChIPResults/ 0 1 0 0
#==============
args <- commandArgs(TRUE)
if(length(args)<1) {
q("no")
}
# directory under which all the results have been stored
# all the subdirectories indicate different samples
# corresponding to the experimental condition mentioned
# in the main directory
baseresdir <- args[1]
# check if the last character of the output base directory is '/'
# unless append that character
if (substr(baseresdir,nchar(baseresdir),nchar(baseresdir)) != '/') {
baseresdir <- paste0(baseresdir, '/')
}
# denotes whether the analysis started from BAM files
# in such a case, FASTQ reads are not available
if (length(args) > 1) {
BAMRead <- as.integer(args[2])
} else {
cat(sprintf("\n User did not provide information whether the BAM file was the starting point -- assuming 0, means that fastq files were used"))
BAMRead <- 0
}
# denotes whether the data samples have been under ChIPMentation method
if (length(args) > 2) {
Tagmentation <- as.integer(args[3])
} else {
cat(sprintf("\n User did not provide information whether the data is ChIPMentation (1) or ChIP seq (0) -- assuming 0"))
Tagmentation <- 0
}
# denotes, if 1, whether old method of summary statistics would be used
if (length(args) > 3) {
OldMethod <- as.integer(args[4])
} else {
OldMethod <- 0
}
# This variable is applicable for new settings only
# 0: peak is derived without any control (default)
# 1: peak is derived with control
# 2: peak is derived with both control and no control
if (length(args) > 4) {
ControlPeak <- as.integer(args[4])
} else {
ControlPeak <- 0
}
#==========================
# following are list of file and directory name conventions which are used in the ChIP seq pipeline
NRFfilenamefmt <- 'out_NRF_MAPQ30.txt'
QCStrandCorrNameFmt <- 'chipSampleMaster.tagAlign.tab'
FRiPFileNameFmt <- 'out_FRiP.txt'
PeakCountFileFmt <- 'Peak_Statistics.txt'
ReadStatFileNameFmt <- 'Read_Count_Stat.txt'
if (OldMethod == 1) {
if (Tagmentation == 1) {
MACS2DirControlNameFmt <- 'MACS2_Tag_with_Control'
MACS2DirNoControlNameFmt <- 'MACS2_Tag_No_Control'
} else {
MACS2DirControlNameFmt <- 'MACS2_with_Control'
MACS2DirNoControlNameFmt <- 'MACS2_No_Control'
}
} else {
if (Tagmentation == 1) {
MACS2DirDefControlNameFmt <- 'MACS2_Default_Tag_with_Control'
MACS2DirExtControlNameFmt <- 'MACS2_Ext_Tag_with_Control'
MACS2DirDefNoControlNameFmt <- 'MACS2_Default_Tag_No_Control'
MACS2DirExtNoControlNameFmt <- 'MACS2_Ext_Tag_No_Control'
} else {
MACS2DirDefControlNameFmt <- 'MACS2_Default_with_Control'
MACS2DirExtControlNameFmt <- 'MACS2_Ext_with_Control'
MACS2DirDefNoControlNameFmt <- 'MACS2_Default_No_Control'
MACS2DirExtNoControlNameFmt <- 'MACS2_Ext_No_Control'
}
}
# output file containing the summary results
if (OldMethod == 1) {
outtextfile <- paste0(baseresdir, 'Results_All_Samples_Summary.txt')
con <- file(outtextfile, "w")
cat(paste(c("Dir", "NumRead", "UniqMappRead", "UniqMapPos", "NRF", "NSC", "RSC", "Qtag", "MappedReadPeak(NoCtrl)", "FRiP(NoCtrl)", "nPeakNoCtrl", "nPeak(Q<0.05)NoCtrl", "nPeak(Q<0.01)NoCtrl", "MappedReadPeak(Ctrl)", "FRiP(Ctrl)", "nPeakCtrl", "nPeak(Q<0.05)Ctrl", "nPeak(Q<0.01)Ctrl"), collapse='\t'), file=con)
} else {
outtextfile <- paste0(baseresdir, 'Results_Summary_NEW.xls')
con <- file(outtextfile, "w")
# initialize the header of the summary excel file
HeaderVec <- c("Dir", "FastqRead", "MappRead")
if (BAMRead == 0) {
HeaderVec <- c(HeaderVec, "%MappRead", "RandomDelRead", "%RandomDelRead", "UniqMappRead", "%UniqMappRead", "MapqThrRead", "%MapqThrRead", "rmDupRead", "%rmDupRead")
} else {
HeaderVec <- c(HeaderVec, "%MappRead(w.r.t FastqRead)", "RandomDelRead", "%RandomDelRead (w.r.t MappRead)", "UniqMappRead", "%UniqMappRead (w.r.t MappRead)", "MapqThrRead", "%MapqThrRead (w.r.t MappRead)", "rmDupRead", "%rmDupRead (w.r.t MappRead)")
}
HeaderVec <- c(HeaderVec, "UniqMapPos", "NRF", "M1", "M2", "PBC1", "PBC2", "NSC", "RSC", "Qtag")
if ((ControlPeak == 0) | (ControlPeak == 2)) {
HeaderVec <- c(HeaderVec, "MappedReadPeak(Def_NoCtrl)", "FRiP(Def_NoCtrl)", "nPeak(Def_NoCtrl)", "nPeak(Q<0.05)(Def_NoCtrl)", "nPeak(Q<0.01)(Def_NoCtrl)", "MappedReadPeak(Ext_NoCtrl)", "FRiP(Ext_NoCtrl)", "nPeak(Ext_NoCtrl)", "nPeak(Q<0.05)(Ext_NoCtrl)", "nPeak(Q<0.01)(Ext_NoCtrl)")
}
if ((ControlPeak == 1) | (ControlPeak == 2)) {
HeaderVec <- c(HeaderVec, "MappedReadPeak(Def_Ctrl)", "FRiP(Def_Ctrl)", "nPeak(Def_Ctrl)", "nPeak(Q<0.05)(Def_Ctrl)", "nPeak(Q<0.01)(Def_Ctrl)", "MappedReadPeak(Ext_Ctrl)", "FRiP(Ext_Ctrl)", "nPeak(Ext_Ctrl)", "nPeak(Q<0.05)(Ext_Ctrl)", "nPeak(Q<0.01)(Ext_Ctrl)")
}
cat(paste(HeaderVec, collapse='\t'), file=con)
}
#=================================
# process individual directories under the main results directory
dir.list <- list.dirs(path = baseresdir, full.names = FALSE, recursive = FALSE)
for (dr in dir.list) {
# condition whether old summary method would be used
if (OldMethod == 0) {
# this vector stores the output results
# same length as the header vector
OutResVec <- rep("NA", length(HeaderVec))
# directory
OutResVec[1] <- basename(dr)
# read the text file containing read count statistic
ReadStatFile <- paste0(baseresdir, dr, "/", ReadStatFileNameFmt)
if (file.exists(ReadStatFile) && (file.access(ReadStatFile, 4) == 0)){
cat(sprintf("\n Found the file: %s \n", ReadStatFile))
x <- readLines(ReadStatFile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
# the line can have 8 or 7 fields
# 8 fields if fastq file is used in the pipeline
# 7 fields if already aligned file is used in the pipeline
nfields <- length(lastline)
cat(sprintf("\n No of fields in the read statistics file: %s ", nfields))
if (BAMRead == 0) {
OutResVec[2] <- lastline[nfields-6] #lastline[2]
OutResVec[3] <- lastline[nfields-5] #lastline[3]
OutResVec[4] <- as.double(OutResVec[3]) / as.double(OutResVec[2])
} else {
OutResVec[3] <- lastline[nfields-5]
}
# RandomDelRead <- lastline[nfields-4]
# Percent_RandomDelRead <- as.double(RandomDelRead) / as.double(OutResVec[2])
OutResVec[5] <- lastline[nfields-3] #lastline[4]
if (BAMRead == 0) {
OutResVec[6] <- as.double(OutResVec[5]) / as.double(OutResVec[2])
} else {
OutResVec[6] <- as.double(OutResVec[5]) / as.double(OutResVec[3])
}
OutResVec[7] <- lastline[nfields-2] #lastline[5]
if (BAMRead == 0) {
OutResVec[8] <- as.double(OutResVec[7]) / as.double(OutResVec[2])
} else {
OutResVec[8] <- as.double(OutResVec[7]) / as.double(OutResVec[3])
}
OutResVec[9] <- lastline[nfields-1] #lastline[6]
if (BAMRead == 0) {
OutResVec[10] <- as.double(OutResVec[9]) / as.double(OutResVec[2])
} else {
OutResVec[10] <- as.double(OutResVec[9]) / as.double(OutResVec[3])
}
OutResVec[11] <- lastline[nfields] #lastline[7]
if (BAMRead == 0) {
OutResVec[12] <- as.double(OutResVec[11]) / as.double(OutResVec[2])
} else {
OutResVec[12] <- as.double(OutResVec[11]) / as.double(OutResVec[3])
}
}
# the following file stores the NRF / library complexity value
NRF_textfile <- paste0(baseresdir, dr, "/", NRFfilenamefmt)
if (file.exists(NRF_textfile) && (file.access(NRF_textfile, 4) == 0)){
# open the file and read line by line
# extract performance values
finp <- file(NRF_textfile, "r")
lineset <- readLines(finp)
for (i in 1:length(lineset)) {
curr_line <- lineset[i]
if (regexpr("Unique_Genome_Pos", curr_line) > 0) {
OutResVec[13] <- as.integer(strsplit(curr_line,":")[[1]][2])
} else if (regexpr("NRF", curr_line) > 0) {
OutResVec[14] <- as.numeric(strsplit(curr_line,":")[[1]][2])
} else if (regexpr("M1", curr_line) > 0) {
OutResVec[15] <- as.integer(strsplit(curr_line,":")[[1]][2])
} else if (regexpr("M2", curr_line) > 0) {
OutResVec[16] <- as.integer(strsplit(curr_line,":")[[1]][2])
} else if (regexpr("PBC1", curr_line) > 0) {
OutResVec[17] <- as.numeric(strsplit(curr_line,":")[[1]][2])
} else if (regexpr("PBC2", curr_line) > 0) {
OutResVec[18] <- as.numeric(strsplit(curr_line,":")[[1]][2])
}
}
# close the input file
close(finp)
}
# following file stores the NSC, RSC, metrics
tabfile <- paste0(baseresdir, dr, "/", QCStrandCorrNameFmt)
if (file.exists(tabfile) && (file.access(tabfile, 4) == 0)){
#print(sprintf("\n Tab text file exists"))
x <- readLines(tabfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[19] <- as.numeric(lastline[9])
OutResVec[20] <- as.numeric(lastline[10])
OutResVec[21] <- as.integer(lastline[11])
}
#=======================================
# insert the peak information
counter <- 22
# peaks when no control is used
if ((ControlPeak == 0) | (ControlPeak == 2)) {
# insert statistics for default MACS2 peaks without control
# FRIP
fripfile <- paste0(baseresdir, dr, "/", MACS2DirDefNoControlNameFmt, "/", FRiPFileNameFmt)
if (file.exists(fripfile) && (file.access(fripfile, 4) == 0)) {
x <- readLines(fripfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[2]
OutResVec[counter+1] <- lastline[3]
}
counter <- counter + 2
# peak count
peakstatfile <- paste0(baseresdir, dr, "/", MACS2DirDefNoControlNameFmt, "/", PeakCountFileFmt)
if (file.exists(peakstatfile) && (file.access(peakstatfile, 4) == 0)) {
x <- readLines(peakstatfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[1]
OutResVec[counter+1] <- lastline[2]
OutResVec[counter+2] <- lastline[3]
}
counter <- counter + 3
# insert statistics for extsize MACS2 peaks without control
# FRIP
fripfile <- paste0(baseresdir, dr, "/", MACS2DirExtNoControlNameFmt, "/", FRiPFileNameFmt)
if (file.exists(fripfile) && (file.access(fripfile, 4) == 0)) {
x <- readLines(fripfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[2]
OutResVec[counter+1] <- lastline[3]
}
counter <- counter + 2
# peak count
peakstatfile <- paste0(baseresdir, dr, "/", MACS2DirExtNoControlNameFmt, "/", PeakCountFileFmt)
if (file.exists(peakstatfile) && (file.access(peakstatfile, 4) == 0)) {
x <- readLines(peakstatfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[1]
OutResVec[counter+1] <- lastline[2]
OutResVec[counter+2] <- lastline[3]
}
counter <- counter + 3
} # end peak check for MACS2 peaks without control
# peaks when control is used
if ((ControlPeak == 1) | (ControlPeak == 2)) {
# insert statistics for default MACS2 peaks with control
# FRIP
fripfile <- paste0(baseresdir, dr, "/", MACS2DirDefControlNameFmt, "/", FRiPFileNameFmt)
if (file.exists(fripfile) && (file.access(fripfile, 4) == 0)) {
x <- readLines(fripfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[2]
OutResVec[counter+1] <- lastline[3]
}
counter <- counter + 2
# peak count
peakstatfile <- paste0(baseresdir, dr, "/", MACS2DirDefControlNameFmt, "/", PeakCountFileFmt)
if (file.exists(peakstatfile) && (file.access(peakstatfile, 4) == 0)) {
x <- readLines(peakstatfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[1]
OutResVec[counter+1] <- lastline[2]
OutResVec[counter+2] <- lastline[3]
}
counter <- counter + 3
# insert statistics for extsize MACS2 peaks with control
# FRIP
fripfile <- paste0(baseresdir, dr, "/", MACS2DirExtControlNameFmt, "/", FRiPFileNameFmt)
if (file.exists(fripfile) && (file.access(fripfile, 4) == 0)) {
x <- readLines(fripfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[2]
OutResVec[counter+1] <- lastline[3]
}
counter <- counter + 2
# peak count
peakstatfile <- paste0(baseresdir, dr, "/", MACS2DirExtControlNameFmt, "/", PeakCountFileFmt)
if (file.exists(peakstatfile) && (file.access(peakstatfile, 4) == 0)) {
x <- readLines(peakstatfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
OutResVec[counter] <- lastline[1]
OutResVec[counter+1] <- lastline[2]
OutResVec[counter+2] <- lastline[3]
}
counter <- counter + 3
} # end peak check for MACS2 peaks with control
# write the statistic in the results log file
cat('\n', paste(OutResVec, collapse='\t'), file=con)
} else {
#==================
# the following file stores the NRF / library complexity value
# at the third column of the last line
#==================
NRF_textfile <- paste0(baseresdir, dr, "/", NRFfilenamefmt)
if (file.exists(NRF_textfile) && (file.access(NRF_textfile, 4) == 0)){
x <- readLines(NRF_textfile)
# the 2nd line in string splitted structure
lastline <- strsplit(x[length(x)], "\t")[[1]]
NumRead <- lastline[1]
UniqMappedRead <- lastline[2]
UniqMappedPos <- lastline[3]
NRF_val <- lastline[4]
} else {
NumRead <- 'NA'
UniqMappedRead <- 'NA'
UniqMappedPos <- 'NA'
NRF_val <- 'NA'
}
#==================
# following file stores the NSC, RSC, metrics
#==================
tabfile <- paste0(baseresdir, dr, "/", QCStrandCorrNameFmt)
if (file.exists(tabfile) && (file.access(tabfile, 4) == 0)){
#print(sprintf("\n Tab text file exists"))
x <- readLines(tabfile)
lastline <- strsplit(x[length(x)], "\t")[[1]]
NSC_val <- lastline[9]
RSC_val <- lastline[10]
Qtag_val <- lastline[11]
} else {
NSC_val <- 'NA'
RSC_val <- 'NA'
Qtag_val <- 'NA'
}
#==================
# FRiP and Peak count measures
# when MACS2 is executed with input control BAM files
#==================
FRiP_textfile_ctrl <- paste0(baseresdir, dr, "/", MACS2DirControlNameFmt, "/", FRiPFileNameFmt)
if (file.exists(FRiP_textfile_ctrl) && (file.access(FRiP_textfile_ctrl, 4) == 0)){
x <- readLines(FRiP_textfile_ctrl)
lastline <- strsplit(x[length(x)], "\t")[[1]]
MappedReadPeakCtrl <- lastline[2]
FRiP_val_ctrl <- lastline[3]
} else {
MappedReadPeakCtrl <- 'NA'
FRiP_val_ctrl <- 'NA'
}
PeakCount_TextFile_ctrl <- paste0(baseresdir, dr, "/", MACS2DirControlNameFmt, "/", PeakCountFileFmt)
if (file.exists(PeakCount_TextFile_ctrl) && (file.access(PeakCount_TextFile_ctrl, 4) == 0)){
x <- readLines(PeakCount_TextFile_ctrl)
lastline <- strsplit(x[length(x)], "\t")[[1]]
TotPeakCtrl <- lastline[1]
TotPeak_Q_Five_Pct_ctrl <- lastline[2]
TotPeak_Q_One_Pct_ctrl <- lastline[3]
} else {
TotPeakCtrl <- 'NA'
TotPeak_Q_Five_Pct_ctrl <- 'NA'
TotPeak_Q_One_Pct_ctrl <- 'NA'
}
#==================
# FRiP and Peak count measures
# when MACS2 is executed with default (without any control bam file)
#==================
FRiP_textfile_Noctrl <- paste0(baseresdir, dr, "/", MACS2DirNoControlNameFmt, "/", FRiPFileNameFmt)
if (file.exists(FRiP_textfile_Noctrl) && (file.access(FRiP_textfile_Noctrl, 4) == 0)){
x <- readLines(FRiP_textfile_Noctrl)
lastline <- strsplit(x[length(x)], "\t")[[1]]
MappedReadPeak <- lastline[2]
FRiP_val <- lastline[3]
} else {
MappedReadPeak <- 'NA'
FRiP_val <- 'NA'
}
PeakCount_TextFile_Noctrl <- paste0(baseresdir, dr, "/", MACS2DirNoControlNameFmt, "/", PeakCountFileFmt)
if (file.exists(PeakCount_TextFile_Noctrl) && (file.access(PeakCount_TextFile_Noctrl, 4) == 0)){
x <- readLines(PeakCount_TextFile_Noctrl)
lastline <- strsplit(x[length(x)], "\t")[[1]]
TotPeak <- lastline[1]
TotPeak_Q_Five_Pct <- lastline[2]
TotPeak_Q_One_Pct <- lastline[3]
} else {
TotPeak <- 'NA'
TotPeak_Q_Five_Pct <- 'NA'
TotPeak_Q_One_Pct <- 'NA'
}
#==============================================
# write the statistic in the results log file
cat('\n', paste(c(basename(dr), NumRead, UniqMappedRead, UniqMappedPos, NRF_val, NSC_val, RSC_val, Qtag_val, MappedReadPeak, FRiP_val, TotPeak, TotPeak_Q_Five_Pct, TotPeak_Q_One_Pct, MappedReadPeakCtrl, FRiP_val_ctrl, TotPeakCtrl, TotPeak_Q_Five_Pct_ctrl, TotPeak_Q_One_Pct_ctrl), collapse='\t'), file=con)
} # end process individual directories
} # end old method condition
if (OldMethod == 0) {
#============================
# a few summary statements for the output text file
#============================
outtext <- paste0("\n\n\n\n\n *** Important parameters ***** \n\n\n")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n FastqRead: number of reads in individual fastq file(s)")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n MappRead: number of mappable reads.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n %MappRead: percentage of mappable reads.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n RandomDelRead: number of reads REMAINING after deleting random chromosome reads.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n %RandomDelRead: percentage of reads REMAINING after deleting random chromosome reads.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n UniqMappRead and %UniqMappRead: number (and percentage) of reads uniquely mapped to the reference genome.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n MapqThrRead and %MapqThrRead: number (and percentage) of reads REMAINING after quality thresholding (default MAPQ=30)")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n rmDupRead and %rmDupRead: number (and percentage) of reads REMAINING after deleting the deplicated reads")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n UniqMapPos: number of distinct genome position where at least one read maps uniquely.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n NRF (Non redundant fraction): number of distinct genome positions for uniquely mapped reads / number of uniquely mapped reads =============== < 0.5: concerning, between 0.5 and 0.8 : acceptable, between 0.8 and 0.9 : compliant, > 0.9: ideal")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n M1: number of genomic locations where exactly one read maps uniquely.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n M2: number of genomic locations where exactly two reads map uniquely.")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n PBC1 (PCR bottlenecking coefficient 1): M1 / UniqMapPos =============== < 0.5: severe bottlenecking level, between 0.5 and 0.8: moderate bottlenecking level, between 0.8 and 0.9 : mild bottlenecking level, >= 0.9 : no bottlenecking ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n PBC2: M1 / M2 =============== < 1: severe bottlenecking level, between 1 and 3: moderate bottlenecking level, between 3 and 10 : mild bottlenecking level, >= 10 : no bottlenecking ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n NSC: Normalized strand correlation --- acceptable if NSC >= 1.05 ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n RSC: relative strand correlation --- acceptable if NSC >= 0.8 ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n Quality tag: negative: reject sample, 0: marginally acceptable, 1: very good sample, 2: excellent quality ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n\n\n\n MACS2 outputs without control input ----- missing values are replaced by NA \n\n")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n MappedReadPeak(NoCtrl): mapped reads in peaks ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n FRiP(NoCtrl): MappedReadPeak(NoCtrl) / UniqMapRead ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n nPeakNoCtrl: number of peaks (determined by p value threshold of 0.01) ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n nPeak(Q<0.05)NoCtrl: number of peaks (determined by q value threshold of 0.05) ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n nPeak(Q<0.01)NoCtrl: number of peaks (determined by q value threshold of 0.01) ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n\n\n\n MACS2 outputs with control input ----- missing values are replaced by NA \n\n")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n MappedReadPeak(Ctrl): mapped reads in peaks ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n FRiP(Ctrl): MappedReadPeak(Ctrl) / UniqMapRead ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n nPeakCtrl: number of peaks (determined by p value threshold of 0.01) ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n nPeak(Q<0.05)Ctrl: number of peaks (determined by q value threshold of 0.05) ")
writeLines(outtext, con=con, sep="\n")
outtext <- paste0("\n\n nPeak(Q<0.01)Ctrl: number of peaks (determined by q value threshold of 0.01) ")
writeLines(outtext, con=con, sep="\n")
} # old method condition
# close the output summary text file
close(con)