...breviation, e.g. “BRCA”.
age_at_initial_pathologic_diagnosis
Age at which a condition or disease was first diagnosed in
years.
anatomic_neoplasm_subdivision
Text term to describe the spatial location, subdivisions
and/or anatomic site name of a tumor.
batch_number
Groups samples by ...
...variants loaded from .bim file.9696 missing IDs set.114 people (0 males, 0 females, 114 ambiguous) loaded from .fam.Ambiguous sex IDs written to LDfiltered.nosex .--extract: 435 variants remaining.Using 1 thread (no multithreaded calculations invoked.Before main variant filters, 114 founders and 0 n...
...ut of 60000 ms;”，请问如何解决，希望详细点。
Prepare data for GoSlim.
8 Sequences send to preform GoSlim: goslim_generic.obo
Error while generating GoSlim results: Error: The host did not accept the connection within timeout of 60000 ms; nested exception is:
org.apache.commons.htt...
...sn't appear to be a GTF file (GFF not supported by this program)
RUN CMD: retrieve_seq_from_fasta.pl --format refGene --seqfile elepant_grass_genome.fa unknown_refGene.txt --out unknown_refGeneMrna.fa
Error: cannot read from regionfile unknown_refGene.txt: No such file or directory
INFO: C...
..._lvl, COG_category, De...
dbl (2): evalue, score
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
...
...tive) position in the distribution. An often used aid is the z-transform which converts the values of a sample into z-scores:
with
zi ... z-transformed sample observationsxi ... original values of the sample... sample means ... standard deviation of the sample
The z-transform is also called...
... association analysis via a mixed linear model (MLM).
A mixed model is one which includes both fixed and random effects. Including random effects gives MLM the
ability to incorporate information about relationships among individuals. When a genetic marker based kinship
matrix (K) is used jointly wit...
...le or directory
awk: cmd. line:1: fatal: cannot open file `B059.cibd.txt' for reading (No such file or directory)
awk: cmd. line:1: fatal: cannot open file `B059.cibd.txt' for reading (No such file or directory)
awk: cmd. line:1: fatal: cannot open file `B083.cibd.txt' for reading (No such file o...
... bias in the data. It is an updated form of the Fisher Strand Test that isbetter at taking into account large amounts of data in high coverage situations. It is used to determine if there is strand bias between forward and reverse strands for the reference or alternate allele. The reported value is...
...r rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post...
...s, sapply, saveRDS, setdiff,
table, tapply, union, unique, unsplit, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
expand.grid, ...
解决办法：
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. seems to be coming from a change in matrixStats 1.2 that released a couple of days ago. Can you downgrade to 1.1 and try?remotes::install_version("matrixStats", version="1.1.0") # ...
...以及他们的区别如下：
In GDC database the clinical data can be retrieved from different sources:
indexed clinical: a refined clinical data that is created using the XML files.XML files: original source of the dataBCR Biotab: tsv files parsed from XML files
There are two main differences ...