Dba object has no peaks

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August undefined, 2024

WebAug 29, 2013 · 46. When you import lib, you're importing the package. The only file to get evaluated and run in this case is the 0 byte __init__.py in the lib directory. If you want access to your function, you can do something like this from lib.mod1 import mod1 and then run the mod12 function like so mod1.mod12 (). If you want to be able to access mod1 when ... WebFeb 1, 2024 · If I replaced the empty/0-peak file into a manually created bed file containing only 1 peak with 0 signal strength, the DBA object can be smoothly created but the step of dba.peakset() got the problem as mentioned. ... As one replicate has no peaks, the …

DBA_OBJECT_USAGE - Oracle Help Center

WebOct 26, 2013 · 1. Oracle is case sensitive. You should probably use an uppercase V in your LIKE clause and change * to %: SELECT * FROM dba_objects WHERE object_name LIKE 'V$%'. Also the correct catalog view name is dba_objects. WebJun 7, 2024 · thanks Rory, I've got this matrix after calling dba.peakset(samples), I guess there is something odd happening when reading my sampleSheet, since I have defined only 4 samples not 5.. 5 Samples, 546816 sites in matrix (2979829 total): ID Condition Replicate Caller Intervals Reads 1 ep_293T_siNeg_R1 siNeg 1 bed 915009 NA 2 … richard king radio announcer

dba.count error in DiffBind

WebMar 1, 2024 · This question was caused by a typo or a problem that can no longer be reproduced. While similar questions may be on-topic here, this one was resolved in a way less likely to help future readers. Closed 3 years ago . WebApr 1, 2024 · It looks like the problem is that most of the class definition is not indented as it should be. Remember that in python indentation is crucial, and is why braces {} are not required. This works for me error-free: class database (object): uri = … WebThere is no reliable way to do this. Even with auditing enabled, indirect object access is not recorded in some cases. For example if you have an ON DELETE CASCADE foreign key defined, and you delete rows from the parent table, the deletion of rows from the child table does not appear in the audit trail.. As far as I know, the only object type that has support … richard king mellon hall of science

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WebApr 2, 2024 · It looks like the problem is that most of the class definition is not indented as it should be. Remember that in python indentation is crucial, and is why braces {} are not required. This works for me error-free: class database (object): uri = "mongodb://127.0.0.1:27017" database = None @staticmethod def initialize (): client = … redline xperienceWebfile. if present, also save the report to a comma separated value (csv) file, using this filename. initString. if saving to a file, pre-pend this string to the filename. ext. if saving to a file, append this extension to the filename. DataType. The class of object for returned report: DBA_DATA_GRANGES. richard king san antonio texas

"WebMar 24, 2024 · If missing, will create a new DBA object based on the sampleSheet. mask: logical or numerical vector indicating which peaksets to include in the resulting model if basing DBA object on an existing one. See dba.mask. minOverlap: only include peaks … " - Dba object has no peaks

Dba object has no peaks

dba.count: Count reads in binding site intervals in …

WebNow retrieve the consensus of these: > ConsensusPeaks <- dba.peakset (ExptConsensus, bRetrieve=TRUE) And pass that in to dba.count (): > Expt <- dba.count (Expt, peaks=ConsensusPeaks) The key is that when you use dba.peakset () with consensus = -DBA_REPLICATE, it adds new peaksets to the DBA object. These peaksets are not … WebNumber of time the k-means algorithm will be run with different centroid seeds. The final results will be the best output of n_init consecutive runs in terms of inertia. metric{“euclidean”, “dtw”, “softdtw”} (default: “euclidean”) Metric to be used for both cluster assignment and barycenter computation. If “dtw”, DBA is used ...

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WebJan 31, 2024 · I've checked in a fix for this (DiffBind_3.6.3).It had to do with specifying minOverlap=0 in the initial call to dba().Did you mean for the consensus peakset used in dba.count() to include all the (merged) peaks? If so you would need to specify minOverlap=0 in the call to dba.count() as well (or instead). Indeed, if you move the … WebMar 24, 2024 · DBA: DBA object peaks: If GRanges, RangedData, dataframe, or matrix, this parameter contains the intervals to use for counting. If character string, it specifies a file containing the intervals to use (with the first three columns specifying chromosome, …

WebApr 10, 2013 · AttributeError: 'function' object has no attribute 'min' then x is a function, and functions (in general) don't have min attributes, so you can't call some_function.min(). What is x? In your code, you've only defined it as . x=var I'm not sure what var is. WebDraws 2-way, 3-way, or 4-way Venn diagrams of overlaps

WebOct 9, 2015 · If you look in dba_tables, the tablespace_name is empty. If you look at the ddl generated with dbms_metadata.get_ddl it shows the tablespace A1 there. There is no segment created for this table as all the partitions contain the data and they are in a different tablespace A2. Webdba: Construct a DBA object dba.analyze: Perform differential binding affinity analysis dba.blacklist: Apply blacklists and/or greylists to peaks (and generate... dba.contrast: Set up contrasts for differential binding affinity analysis dba.count: Count reads in binding site intervals dba.load: load DBA object dba.mask: Derive a mask to define a subset of …

WebALL_OBJECTS shows all objects of current and those object which you have rights to access. DBA_OBJECTS shows all object of all users . My question is, if you have DBA role, should ALL_OBJECTS be equal to DBA_OBJECTS? I have DBA role and in the …

WebMar 24, 2024 · dba: Construct a DBA object dba.analyze: Perform differential binding affinity analysis dba.blacklist: Apply blacklists and/or greylists to peaks (and generate... dba.contrast: Set up contrasts for differential binding affinity analysis dba.count: Count reads in binding site intervals dba.load: load DBA object dba.mask: Derive a mask to define a … richard kingscote jockey twitterWebMay 17, 2024 · the sampleMetadata.df I have in my code is indeed a data frame, I didnt mention this explicitly enough but it was never a dba object. This is why I shared the dba object so you can reproduce. The documentation for ?dba.peakset says for minOverlap: "the minimum number of peaksets a peak must be in to be included when adding a … redline wrecker dallas gaWebFeb 1, 2024 · You can run file.info() on the Peaks files, eg file.info("zh11_drought_01_peaks.xls") For each peak file, to make sure they are all there with read access and actual data inside. redline wrecker serviceWebscore. which score to use in the binding affinity matrix. Note that all raw read counts are maintained for use by dba.analyze, regardless of how this is set. One of: DBA_SCORE_READS. raw read count for interval using only reads from ChIP. … richard kingscote jockey ageWebFeb 7, 2024 · You use the Database object and its methods and properties to manipulate an open database. In any type of database, you can: Use the Execute method to run an action query. Set the Connect property to establish a connection to an ODBC data source. Set the QueryTimeout property to limit the length of time to wait for a query to execute … richard king of rockWebJul 28, 2024 · To do this, run the following as SYSDBA in SQL*Plus: set linesize 200 trimspool on set pagesize 2000 col owner form a30 col created form a25 col last_ddl_time form a25 col object_name form a30 col object_type form a25 select OWNER,OBJECT_NAME,OBJECT_TYPE, status, to_char(CREATED,'dd-mon-yyyy … redline xtreme deathWebUSER_OBJECT_USAGE displays statistics about index usage gathered from the database for the indexes owned by the current user. Indicates whether the monitoring feature is turned on. Possible values: Indicates whether the index has been accessed. Possible values: Start monitoring time in sys.object_stats.start_monitoring. redline x ray training